Sediment Transport in San Pablo Bay

Transcription

1 Chapter 2 Sediment Transport in San Pablo Bay By David H. Schoellhamer, Neil K. Ganju, and Gregory G. Shellenbarger Introduction San Pablo Bay is the northwestern subembayment of the San Francisco Estuary (fig. 1). A deepwater (deeper than 12 m) shipping channel runs through the southern half of San Pablo Bay between San Pablo Strait and Carquinez Strait. A minor navigation channel is maintained between San Pablo Bay and the Petaluma River, with maximum depths of 7 m. The remainder of the bay is relatively broad and shallow, with depths less than 4 m. Numerous mudflats on the periphery of the bay are exposed at low tide. Saline water is supplied by the Pacific Ocean by way of the Golden Gate, while the Sacramento/San Joaquin River Delta (Delta) provides the majority of freshwater. Several minor tributaries also feed San Pablo Bay, including the Petaluma River and Sonoma Creek/Second Napa Slough (SNS). Freshwater flow to San Pablo Bay primarily occurs during winter rains, spring snowmelt runoff, and reservoir releases. Low freshwater flow conditions prevail from late spring to early fall. The mixed diurnal and semidiurnal tidal forcing from the Pacific Ocean results in a maximum spring tide range of 2.5 m, and a minimum neap tide range of 0.4 m. Onshore west-northwest winds during the summer months generate wind waves and sediment resuspension (Krone, 1979; Ruhl and others, 2001). 1

2 During winter storms, winds are southerly and generate waves that resuspend sediment along the northern shores of San Pablo Bay. Bed and suspended sediments mostly consist of silts and clays, while sand is in the deeper channels (Conomos and Peterson, 1977). Clays and finer silts are cohesive and combine to form flocs when suspended. Flocs are composed of many particles, often are bound by organic matter and secretions, contain pore space, are less dense, and have a greater settling velocity than do individual particles. Kineke and Sternberg (1989) found that flocs in San Pablo Bay commonly had a diameter of about 100 microns and had a settling velocity of 0.05 to 0.20 centimeters per second (cm/s). Krank and Milligan (1992) found that the population of small flocs remained fairly constant through a tidal cycle in San Pablo Bay, but the number of large flocs increased with the suspended-sediment concentration (SSC). Krone (1979) suggests that suspended-sediment transport within San Pablo Bay follows a seasonal cycle: the majority of suspended sediment is delivered through the Delta during the large, winter freshwater flows, creating a large pool of erodible sediment within the channels and shallows. During the following summer months, persistent onshore winds generate wind waves, resuspending bed sediments in the shallows for transport by tidal currents. Sediment most likely is transported away from high energy areas (mudflats and shallow off-channel areas, for example) to lower energy areas (continental shelf, marinas, deep channels, and marsh surfaces, for example). As the summer progresses, the finer fraction of this erodible pool is reduced. In the fall, when neither wind nor freshwater flow is significant, SSC is at its lowest. As the wet season commences during winter, the cycle repeats itself. In this chapter we summarize recent findings that largely corroborate this conceptual model and provide additional details of sediment transport in San Pablo Bay. 2

3 Sediment Supply and Loss Sediment can enter San Pablo Bay from Carquinez Strait, tributary streams, and Central Bay. Sediment can exit San Pablo Bay to Carquinez Strait and Central Bay. Deposition on tidal marsh or the bottom of San Pablo Bay can be considered a loss of suspended sediment from San Pablo Bay, while erosion from the bottom can be considered a supply of suspended sediment. Carquinez Strait Carquinez Strait connects the deep channel of San Pablo Bay to Suisun Bay, the Delta, and Central Valley watershed. Freshwater flow from the Central Valley typically is an order of magnitude greater than flow from tributary streams that directly enter San Pablo Bay. Thus, Carquinez Strait acts as the landward boundary of San Pablo Bay. Ganju and Schoellhamer (2006) measured SSC at four points, velocity-weighted SSC, watervelocity profiles, and water discharge to calculate suspended-sediment flux (mass/time) at Benicia, the eastern (landward) boundary of Carquinez Strait. Velocity-weighted SSC in a cross section is calculated as uc da SSC u = (1) u da where A is channel area, and u and c are velocity and suspended-sediment concentration. Assuming that deposition and erosion in Carquinez Strait are small, Benicia fluxes will approximate fluxes from Carquinez Strait into San Pablo Bay. The small surface area of Carquinez Strait compared to San Pablo and Suisun Bays and the coarse bottom sediment in the Strait (Conomos and Peterson, 1977) support this assumption. 3

4 The decomposition of the total constituent flux is given by Dyer (1974). Lateral and vertical variations of SSC in the channel can be ignored because SSC u is assumed to account for cross-sectional variability. Thus, the flux equation reduces to: [F] = [U][A][SSC u ] + U'[A][SSC u ] + [U]A'[SSC u ] + U' A'[SSC u ] + [U][A]SSC u ' + U'[A]SSC u ' + [U]A' SSC u ' + U' A' SSC u ' (2) where [F] is the total discharge weighted residual suspended sediment flux, U is the channelaverage velocity, A is the channel area, and SSC u is the velocity-weighted SSC. Brackets denote a tidally averaged value, while the prime indicates the temporal deviation of the instantaneous value from the tidally averaged value such that x=[x]+x. Tidal averaging was performed using a low-pass Butterworth filter with a cutoff frequency of 1/30 h -1. The filter was applied in the forward and reverse directions to minimize anomalies at the endpoints of the record. Typically, the advective and dispersive flux terms (eq. 2, terms 1 and 6 respectively) are the largest components of total flux, while Stokes drift (eq. 2, term 4) is a minor component. Advective flux quantifies the contribution of tidally averaged discharge and concentration (caused by river flow, for example), while dispersive flux represents the correlation between velocity and concentration fluctuations. Stokes drift accounts for the correlation of velocity and area, which is upstream for a progressive tidal wave. The remaining terms usually are negligible (Ganju and Schoellhamer, 2006). During periods of large freshwater discharge from the Central Valley, Carquinez Strait delivers sediment to San Pablo Bay. In April 2004, for example, freshwater flow, total flux, advective flux, and dispersive flux usually were large and directed seaward into San Pablo Bay (fig. 2). 4

5 During periods of small freshwater discharge from the Central Valley, sediment moves from San Pablo Bay into Carquinez Strait. In May and June 2004, for example, advective flux was minimal, while dispersive and total fluxes were landward (fig. 2). Properties of saltwater and wind-wave resuspension caused this landward transport. Salinity is greatest near the ocean and smallest near the rivers. This difference in longitudinal salinity (gradient) from the rivers to the ocean can cause the tidally averaged currents to flow landward along the bottom and seaward along the surface (gravitational circulation, Burau and others, 1993; Schoellhamer and Burau, 1998). Saltwater also is denser than freshwater; therefore, saltier water tends to be near the bottom of estuaries. The difference in the amount of salinity between the top and bottom of the water column (stratification) can be great enough to prevent the top and bottom waters from mixing. Stratification can trap suspended sediment in the lower water column where tidally averaged transport is landward. Stratification also can dampen turbulence in the water column and allow suspended sediment to settle. Turbulence during flood tide typically is greater than during ebb tide, favoring flood (landward) transport of suspended sediment (Monismith and others, 1996; Schoellhamer, 2001a). Wind-wave resuspension of bottom sediment in the shallows of San Pablo Bay (discussed elsewhere in this report), provides a source of suspended sediment that moves into Carquinez Strait on flood tide. There is little wind-wave resuspension in Carquinez Strait because it is relatively deep. Ganju and Schoellhamer (2006) used surrogate measurements for advective, dispersive, and Stokes drift flux to estimate annual suspended-sediment flux through Carquinez Strait. The surrogates were upstream watershed discharge, suspended-sediment concentration at one location in the Strait, and the longitudinal salinity gradient. The first two surrogates substituted for tidally averaged discharge and velocity-weighted suspended-sediment concentration in the Strait, and the product of the two thereby provided advective flux estimates. Dispersive flux was estimated using the product of longitudinal salinity gradient and the root-mean-square of velocity-weighted suspended-sediment concentration. 5

6 Stokes drift was estimated with suspended-sediment concentration alone. Cross-sectional measurements validated the use of surrogates during the monitoring period. Estimates of yearly sediment fluxes through Carquinez Strait had large variability, partly because the freshwater flows were highly variable (table 1). The data indicate that large amounts of sediment were transported to San Pablo Bay only during years of large freshwater flow. Sediment transport into San Pablo Bay was particularly large in 1998, when freshwater flow and low salinity gradient persisted through most of the summer months. As a result, the strength of gravitational circulation in Carquinez Strait possibly was reduced, and the net dispersive flux was seaward. In all other years of data collection, the net dispersive flux was landward. During years of low freshwater flow, seaward advective transport was relatively small and was exceeded by the landward dispersive transport in Thus, net annual sediment transport in 2002 was out of San Pablo Bay into Carquinez Strait. The error involved with the dispersive flux prediction is larger than advective and Stokes drift flux predictions, therefore differences in total dispersive flux between water years are relatively uncertain. However the net direction of these fluxes clearly is modulated by residual flow and sediment concentrations, as extreme years such as 1998 and 2002 demonstrate. 6

7 Tributary streams Porterfield (1980) conducted an extensive study of sediment transport to San Francisco Bay, including San Pablo Bay, from tributary streams. In the San Pablo Bay watershed, sediment discharge data were collected on the Napa River at St. Helena (USGS station number , drainage area 81.4 mi 2 ) and Sonoma Creek at Boyes Hot Springs (station , drainage area 62.2 mi 2, called Agua Caliente beginning in water year 1967) during Sediment-rating curves, which define the relation between water discharge and sediment discharge, were determined using data (table 2). Suspended-sediment discharge and total-sediment discharge, which includes bedload, were determined. Sediment discharge during was determined by applying the sediment transport curves to the flow-duration curve. The sediment yield of stream basins and areas for which no sediment data were available was estimated on the basis of sediment yield from adjacent basins with similar hydraulic characteristics. The total drainage area into San Pablo Bay is 962 mi 2 of which 610 mi 2 contribute to the sediment supply. Sediment supply from mi 2 (24 percent of the contributing area) was measured and mi 2 (76 percent) was estimated. Two sources of uncertainty in applying the Porterfield (1980) estimates to present (2006) tributary sediment transport are the large unmeasured area and land-use change. Only about 31 percent of the estimated tributary sediment supply to San Pablo Bay was measured and 69 percent was estimated. Land use has changed since the late 1950s, which is likely to change sediment yield from the watershed. 7

8 Additional data are available from the Napa River to evaluate these uncertainties. Suspendedsediment discharge was measured several times a year in the Napa River at Napa (station , drainage area 218 mi 2 ) downstream from the St. Helena station for water years 1971 and A sediment rating curve was developed from the data (Glysson, 1987) and applied to measured daily flows to estimate daily suspended-sediment discharge. Typically, daily sediment samples would be collected to develop a daily suspended-sediment discharge record, so the accuracy of the estimated daily record at this station is less than typical. The estimated mean daily suspended-sediment discharge was 3.7 kg/s (360 ton/d, 0.12 Mt/yr) and varied kg/s. Sediment yield was 1.6 ton/d/mi 2, which is slightly less than 2.1 ton/d/mi 2 calculated by Porterfield (1980) for the St. Helena site for the period. Given the different time periods and stations on the Napa River, these sediment yields are not directly comparable, but their similarity indicates that sediment yield did not change tremendously during the 20th century and that qualitative conclusions from analysis of Porterfield s data still are applicable. The sediment supply to San Pablo Bay from tributaries is much smaller than from Carquinez Strait. Based on the Porterfield data (1980) in table 2, the largest estimate of average tributary sediment supply is 831 ton/d, which is equal to 0.28 Mt/yr. The mean sediment flux from Carquinez Strait from the data in table 1 is 4.8 Mt/yr. Eliminating the large value for water year 1998 gives a mean sediment flux from Carquinez Strait of 0.76 Mt/yr, which almost is three times larger than the average tributary supply. Although these estimates are based on data from different periods, this comparison demonstrates the relative importance of sediment supply from Carquinez Strait, compared to that from tributary streams. 8

9 Net bottom erosion or deposition The bottom of San Pablo Bay is a source of suspended sediment when it erodes and a sink for suspended sediment when there is net deposition. Jaffe and others (2007) used bathymetric surveys to calculate that San Pablo Bay eroded an average of a 700,000±100,000 m 3 /yr from 1951 to 1983, which are the most recent data available. Jaffe (USGS, written communication, 2006) measured a dry bulk density of bottom sediment in San Pablo Bay of 646 kg/m 3. Multiplying the volumetric erosion rate by the bulk density gives a mass erosion rate of 0.45 Mt/yr. This value is between the estimated supplies from Carquinez Strait (0.76 Mt/yr) and local tributaries (0.28 Mt/yr). Dredged material disposal San Pablo Bay contains two dredged material disposal sites, SF9 and SF10. Material that is dredged elsewhere and disposed of in San Pablo Bay would be a supply of sediment to San Pablo Bay. Material that is dredged in San Pablo Bay and disposed of elsewhere would be a loss from San Pablo Bay. Material dredged from and disposed in San Pablo Bay would be neither a supply nor loss of sediment. 9

10 Records from the U.S. Army Corps of Engineers, San Francisco District, were used to determine dredged material disposal volumes for the period The mean annual disposal in San Pablo Bay was 450,000 m 3 (reported as 5.9 million yd 3 over 10 years). Twenty-one percent of this volume came from outside San Pablo Bay. Smith (1963) reported that the average bulk density of dredged spoil in San Pablo Bay was 31 lb/ft 3 or 497 kg/m 3. The total mass of dredged material disposed of in San Pablo Bay was 0.22 Mt/yr and the mass from outside San Pablo Bay was 0.05 Mt/yr. The only record we could find of material from San Pablo Bay being disposed of outside the Bay was 160,000 m 3 from the Petaluma River channel disposed of at an upland site in During the 10-year period, the mean annual export of dredged material is 0.01 Mt/yr. The net import of dredged material to San Pablo Bay was 0.04 Mt/yr. This source is smaller than other sources (Carquinez Strait, tributary streams, and bottom erosion). For this calculation, we consider Mare Island Strait to be part of San Pablo Bay. Krone (1960) used a radioactive tracer to conservatively estimate that 8 percent of the sediment disposed at SF9 deposits in Mare Island Strait in only 2 3 days. There also was a large bottom plume of disposed sediment in Carquinez Strait that had moved toward Mare Island Strait. We have no measurement of this transport from SF9 to Mare Island Strait because our flux measurement boundary is further east at Benicia. Thus, we have no method to account for transport from SF9 to Mare Island Strait, so we assume Mare Island Strait is part of San Pablo Bay to conserve mass for a subsequent sediment budget calculation. In addition, dredging of Mare Island Strait greatly decreased during the 1990s when a naval base on the Strait closed, so this dredging is not indicative of conditions after the late 1990s. If Mare Island Strait was considered outside San Pablo Bay, 63 percent of sediment disposed of in San Pablo Bay would have come from elsewhere. 10

11 Deposition on tidal marsh The yearly net volume of sediment that deposits on tidal marshes can be estimated by multiplying the rate of sea level rise by the total area of the tidal marsh. This assumes that the marsh accretes sediment at a rate to maintain its elevation relative to sea level. The Baylands Ecosystem Habitat Goals Project Report (1999) estimates that in 1988 there were 65 km 2 of tidal marsh habitat adjacent to San Pablo Bay. The report defines tidal marshes as being vegetated, subject to tidal action, and ranging from the lowest extent of vascular plants to the maximum height of the tide. Flick and others (2003) estimate that sea level rise in San Francisco Bay was 2.14 mm/yr during the 20th century. The resulting deposition volume is 140,000 m 3 /yr. The mean bulk density of San Pablo Bay tidal marsh sediments from nine samples collected by Denise Reed (University of New Orleans, written communication, 2003) was 592 kg/m 3. Multiplying the deposition volume by the bulk density gives a deposition mass of 0.08 Mt/yr. This loss is less than the supply from Carquinez Strait, tributary streams, or bottom erosion and greater than the net supply from dredged material disposal. Central Bay San Pablo Strait connects San Pablo Bay to Central Bay (fig. 1). SSC has been measured in the Strait at site Point San Pablo (PSP) since December 1992 (Buchanan and Lionberger, 2006), but not suspended-sediment flux (mass per time or kg/s). In this report we analyze SSC measurements at PSP, but we cannot determine the suspended-sediment flux in San Pablo Strait from the measurements. 11

12 The mass of sediment moving from San Pablo Bay to Central Bay can be estimated by applying the principle of conservation of mass to our estimates of sediment supplied from Carquinez Strait, tributaries, bottom erosion, and imported dredged material and sediment lost to deposition on tidal marshes. For mass to be conserved, the mass of sediment lost to Central Bay must equal the sum of all of these sources. Sediment supply and loss estimates are from different time periods (table 3), which introduces an error in addition to the errors of each individual estimate. The mean annual sediment transport from San Pablo Bay to Central Bay is 1.45 Mt/yr. The physical processes that transport sediment in San Pablo Strait are similar to those described in Carquinez Strait and can be used to develop a qualitative description of sediment transport in San Pablo Strait. Large freshwater pulses from the Central Valley increase seaward advective flux and transport sediment seaward. Wind-wave resuspension and SSC in San Pablo Bay are greater than in Central Bay (Ruhl and others, 2001). The resulting concentration gradient would result in a dispersive flux from San Pablo Bay to Central Bay. Gravitational circulation, however, results in a dispersive flux in the opposite direction. Whether the net dispersive flux is seaward or landward in San Pablo Strait is unknown. Interaction of San Pablo Bay with its Tributary Streams Tides propagate through San Pablo Bay and up into the lower reaches of tributary streams. Sills and small tidal excursions, however, can limit the amount of sediment the sloshing tides transport between the Bay and tributary streams (Napa Marsh, Sonoma Creek, and Petaluma River). Some of the tributaries that supply sediment to the Bay during high flows act as sediment traps during low flows. Thus, sediment transport in tributary streams has varying degrees of connection to and isolation from San Pablo Bay. In this section of the report, we present examples of how sediment transport is affected by the tidal interaction of San Pablo Bay with its tributary streams. 12

13 Barotropic convergence in Napa/Sonoma Marsh The Napa/Sonoma Marsh is a network of tidal sloughs that surround several islands north of San Pablo Bay (fig. 3). The sloughs are connected to Sonoma Creek to the west and the Napa River to the east, both of which connect to San Pablo Bay. The tidal wave propagating landward through San Pablo Bay enters the marsh from the west (Sonoma Creek) and the east (Napa River). For example, during flood tide, water on the west side of South Slough is flowing to the east and water on the east side of the Slough is flowing to the west (fig. 3). In the approximate middle of the slough and marsh, these flood currents converge and the water velocity is negligible. Warner and others (2003) called this area the barotropic convergence zone. Sediment accumulates in the barotropic convergence zone. The zone is within one tidal excursion from San Pablo Bay and most of the sloughs have narrowed due to advection of sediment from San Pablo Bay during flood tide, deposition of the sediment, and subsequent lack of shear stress on the ebb that is large enough to resuspend the sediment (Warner and others, 2003). Most of the sloughs in the barotropic convergence zone are shallow, narrow, vegetation-choked channels compared to the sloughs closer to Sonoma Creek and Napa River outside the zone. In addition to sediment accumulation, Swanson and others (2003) found that after the breach of a salt pond widened in December 2002, a pulse of saline water remained in the barotropic convergence zone for 10 days while salinity was smaller elsewhere. A sill at the mouth of Sonoma Creek becomes exposed during low spring tides, truncating the tide on the west side of the marsh (Warner and others, 2003). During spring tides, tidally averaged water-surface elevations are higher on the west side, which causes easterly, tidally averaged fluxes of water and sediment. During neap tides, the sill is not exposed at low tide and the west side of the marsh experiences the full tide range, creating tidally averaged fluxes in the opposite direction. 13

14 Baroclinic convergence in Mare Island Strait The lower Napa River becomes Mare Island Strait just before the junction with the western end of Carquinez Strait and eastern end of San Pablo Bay. Whereas converging tidal currents trap and deposit suspended sediment in the Napa/Sonoma Marsh, the phasing of the tidal currents in the two straits creates a salinity minimum in Mare Island Strait in which suspended sediment converges and deposits (Warner and others, 2002). The tide turns in Mare Island Strait before Carquinez Strait, so Mare Island Strait is at slack tide while Carquinez Strait is still flooding (fig. 4A). Mare Island Strait begins to flood while Carquinez Strait is still ebbing, and the salinity of water entering Mare Island Strait decreases with time (fig. 4B). About 2 hours later, Carquinez Strait begins to flood and the salinity of water entering Mare Island Strait begins to increase with time (fig. 4C). The result is that a local salinity minimum propagates up Mare Island Strait. This occurs most of the year when freshwater flow in the Napa River is low. Gravitational circulation occurs during moderate flows and tidally averaged currents are seaward during large flows. As mentioned previously, tidally averaged currents will flow toward lower salinity (usually landward) along the bottom and toward higher salinity along the surface. This creates gravitational circulation that transports suspended sediment landward because SSC is greater near the bottom. The salinity minimum in Mare Island Strait complicates sediment transport. Tidally averaged near-bottom currents are directed toward lower salinity, so landward and seaward from the salinity minimum tidally averaged bottom currents are directed towards the salinity minimum. The result is that suspended sediment converges and deposits in the salinity minimum. Warner and others (2002) called this a baroclinic convergence zone. This convergence and a supply of suspended sediment from Carquinez Strait and San Pablo Bay, probably account for the exceptional rates of sediment accumulation historically observed in Mare Island Strait. 14

15 The baroclinic convergence zone also appears to explain the spatial distribution of selenium contamination in clams in Mare Island Strait. Linville and others (2002) found that the invasive clam Potamocorbula amurensis bioaccumulates selenium and that selenium concentrations in clams increased as residence time increased. In October 1995, selenium concentrations in clams in Mare Island Strait were greatest at the tidally averaged position of the salinity minimum near channel marker 2 and smaller landward and seaward (Linville and others, 2002; table 1). The source of selenium primarily was refineries located in Carquinez Strait and Suisun Bay, so convergent transport and not a local source must be responsible for the clam selenium maximum in Mare Island Strait. Tidally oscillating sediment masses in Petaluma River and Sonoma Creek To study the interaction of Petaluma River and Sonoma Creek/Second Napa Slough (SNS) tributary systems with San Pablo Bay, each tributary system was occupied by two equipment sites consisting of conductivity, temperature, depth, and optical sensors (Ganju and others, 2004). Velocity meters were present at all sites except site channel marker 9 (CM9, fig. 1). Site Pet was located within the Petaluma River and site CM9 occupied the dredged Petaluma River entrance channel in San Pablo Bay. Site SNS was situated within the slough network of northeast San Pablo Bay, upstream from the mouth of Sonoma Creek. Though site SNS is not in Sonoma Creek proper, water is transported regularly with the tides from Sonoma Creek to SNS. Site Pablo was located at the mouth of Sonoma Creek. 15

16 The existence of an oscillating sediment mass in the Petaluma River and Sonoma Creek is suggested by the time-series of SSC at sites Pet and CM9 (fig. 5) and sites SNS and Pablo (fig. 6). The geometry and tidal currents in the area create a process of sediment erosion and deposition that repeats with each tidal cycle (about every 12.4 hours). As water flows seaward on ebb tides, the tidal currents apply force to the river bed. Deposits of sediment on the bed near the landward sites (sites Pet and SNS) eroded and mixed into the water column. As this resuspended-sediment mass moves downstream, SSC is very high (greater than 500 mg/l). Once the suspended-sediment mass reaches the seaward sites (CM9 and Pablo), slack tide and the broad area allow sediment to drop out of the water, forming a seaward sediment deposit. As water begins flowing landward immediately after the tide turns from slack to flood, the seaward sediment deposits are resuspended and transported landward. This process then repeats, with the same sediment mass oscillating back and forth between the rivers and San Pablo Bay. Sediment effectively is trapped within these areas, except during large freshwater flows from the rivers (Ganju and others, 2004). The tidal oscillation of sediment between the landward sites and the seaward sites is independent of the SSC variability observed closest to the open boundaries of San Pablo Bay at sites PSP and Ben (tile 4 in figs. 5 and 6). Sites PSP and Ben are equipped with two sets of sensors at different depths. For this comparison, the near-bottom sensor data are presented because they have the greatest SSC at these sites. 16

17 Wind and wind-wave resuspension in San Pablo Bay are not major factors in the transport processes described here because the mobilization and deposition of the mobile mass occurs independently from wind events. While sediment in the mobile mass is more likely to stay in suspension when wind waves are present, the magnitude of the advected and resuspended sediment concentrations are more a function of tidal currents and spring/neap variability than of wind. Despite higher wind speeds between November 4 10, 2000, SSC is greatest during the strongest ebb tides, between November 11 17, 2000 (fig. 7). The combination of stronger currents and larger tidal excursion create a larger mobile mass that is able to reach site CM9 from the Petaluma River during ebb tides. During the prevalent low-flow conditions, the major factors that create tidally oscillating sediment are geometry and tidal ranges/velocities. Assuming that the ocean and deep water channel are permanent sediment sinks, the geometric isolation of suspended sediment in the river/bay system allow the mass to persist. Mean ebb tidal excursion at site Pet (6 km) is less than the distance to the deep channel (19 km), indicating that sediments only can reach the permanent sink during strong ebb tides or episodic river discharge, as is the case with the Sonoma Creek/SNS system. The sediment mass in both cases is unable to consistently advect to the permanent sink (channel/open ocean), thereby promoting sediment retention within the system. Seaward tidal flats in the systems mentioned may assist in controlling further downstream/ebb transport. 17

18 OBSERVED SEDIMENT TRANSPORT IN SAN PABLO BAY Water depth in San Pablo Bay increases as one moves from tidally exposed mudflats adjacent to the shoreline to the ship channel near the southern shore that is up to 22 m deep. Wind waves are generated in San Pablo Bay and produce orbital water motion that diminishes with depth below the water surface. In shallow water, this orbital motion reaches the bottom, applies a shear stress to the bed, and can resuspend sediment. In deep water, orbital motion is insignificant at the bed and does not resuspend sediment. Tidal currents also can resuspend sediment. These currents are greatest in the deep channel (more than 100 cm/s) and diminish in shallower water (20 cm/s, Cheng and Gartner, 1984). Tidal currents also transport suspended sediment. In this section we describe sediment transport at different water depths in San Pablo Bay by presenting observations of sediment transport in shallow water (2.4 m MLLW, channel marker 1) seaward of the oscillating sediment masses in tributary streams, at the edge of the deep channel (5 m) near the proposed aquatic transfer facility (ATF) site, and from the deep channel (7.9 m) at Point San Pablo. SSC variations at tidal to interannual time scales are discussed. 18

19 Channel Marker 1, To obtain SSC data from shallow water of San Pablo Bay outside the influence of the tidally oscillating sediment mass at CM9, a YSI 6920 multiprobe (equipped with conductivity, temperature, depth, and optical sensors) was located at a channel marker (site CM1) marking the approach to the Petaluma River channel (fig. 1) from November 18, 2003, to September 30, Water depth was 2.4 m MLLW. Multiprobes also were in operation in Carquinez Strait (site Car) and at PSP, with two sensors at differing vertical levels in the water column at each location (table 4). Data were collected at 15-minute intervals. Despite use of a wiper mechanism intended to prevent biological fouling of the optical probe at CM1, data loss from fouling occurred and only 54 percent of the data were valid. Water samples collected at the location of the sensor were used to calibrate the optical sensor output to SSC. While freshwater flow and accompanying sediment loads increased SSC at site Car, the responses at sites CM1 and PSP were less pronounced. For example, increased freshwater flow between February and April 2004 elevated SSC at site Car on the tidal and tidally averaged timescale, yet SSC at site CM1 and, to a lesser extent, site PSP responded more to the associated storm winds (figs. 8 and 9). A likely explanation is that site Car is in Carquinez Strait, which is the main conduit between the Central Valley watershed and San Pablo Bay, while CM1 is more than 3 km from the deep channel and PSP is at the seaward boundary of San Pablo Bay. 19

20 Though increased freshwater flow has little effect on SSC at site CM1, winds associated with episodic storms tend to elevate SSC. Wave data for this area are not available, but the large fetch and shallow depth in San Pablo Bay suggests that episodic winds exceeding 5 m/s are capable of creating wind waves that are able to increase bottom shear stress significantly. In fact, peak SSC at site CM1 were observed during wind events in late February 2004 (figs. 8 and 9). Site PSP data indicated advection of turbid water from San Pablo Bay during these episodic winds (fig. 10). By contrast, site Car did not respond to episodic winds, perhaps due to the limited flood tide excursions between the flats of San Pablo Bay and Carquinez Strait. Sites PSP and Car are too deep for wind waves to resuspend bottom sediment. SSC is greater during strong winter wind than during equivalent summer wind and SSC is greatest in winter and smallest in autumn (table 5). Two possible explanations are differences in wind direction and sediment erodibility. Winds that accompany east-moving cold fronts typically arrive from a south-southwest direction, whereas the diurnal summer winds arrive from the west. This difference in orientation changes the fetch over the flats in San Pablo Bay; the fetch is 16 km for a westerly wind, while it is 19 km for a southwesterly wind. This increase in fetch may induce an increase in wave height and, therefore, near-bottom velocity, which may induce a greater bed-shear stress and increased resuspension. Increased erodibility in winter also may be a function of particle size or biostabilization. According to the Krone (1979) conceptual model, the more erodible fine sediments are winnowed from the bed from winter to summer, which would result in a less erodible bed during summer. In addition, seasonal changes in benthic composition, such as densities of clams, may affect the stability of the bed. Poulton and others (2004) suggested that increased predation of the clam Corbula by diving ducks and sturgeon reduced densities during the winter months of Disruption of the bottom by predators may increase erodibility during winter. In addition, Crimaldi and others (2002) hypothesize 20

21 that denser Corbula communities stabilize bed sediment and thus greater density during summer would decrease erodibility compared to winter. The tidal currents throughout San Pablo Bay increase SSC on both tidal and spring-neap timescales, though the magnitude of SSC is modulated by wave resuspension as well. Tidal advection and resuspension of sediment are observed at all sites, though the magnitude of the fluctuation is dictated by sediment supply (site Car), wind energy (site CM1), and the spring-neap tidal cycle (site PSP). 21

22 Vicinity of proposed Aquatic Transfer Facility, Methods In October 2005, a monitoring site (SPB) was established in the vicinity of the proposed Aquatic Transfer Facility at the edge of the deep channel. A conductivity, temperature, depth, and turbidity sonde (CTDT, YSI Incorporated) was deployed adjacent to an upward-looking 600 khz acoustic Doppler current profiler (ADCP, RD Instruments). Both instruments were deployed on separate moorings (figs. 11 and 12) in the vicinity of 38º01.15' N and 122º25.10' W, northeast of the SF10 dredged material disposal site. The instruments were deployed in about 5 m of water (at MLLW). The CTDT was positioned to sample 2 m above the bottom. This corresponds to the same depth as one of the ADCP measurement bins, which allows for the calculation of sediment point flux 2 m above the bed. Water-velocity profiles and CTDT data are collected simultaneously every 15 minutes. The ADCP is operated in mode 1 with 120 pings per 2-minute ensemble with 25-cm-tall bins. The ADCP is equipped with the waves package, which measures significant wave height, wave direction, and wave period in 20-minute bursts each hour. The CTDT package was recovered every 3 4 weeks to download data and calibrate and clean the sonde. Water samples to calibrate the optical probe for suspended-sediment concentration were collected 2 m above the bottom near the sonde after cleaning and redeployment. The ADCP originally was deployed for 3-month intervals, but because of problems with data loss, the deployment interval was reduced to 6 8 weeks. The instrument package was recovered and taken back to shore for downloading data, cleaning, testing, and replacing the batteries, if necessary. 22

23 Three problems were responsible for the majority of the ADCP data loss. The first problem was that rapid currents tilted the ADCP beyond its allowable range because the instrument had too little weight for the double gimbal in which it was mounted. This was corrected on March 7, 2006, by locking the gimbal. This does not create a problem for the deployments because the bathymetry of this area of San Pablo Bay is flat enough that the instrument can remain level (within three degrees of vertical) to collect valid data with the gimbal locked. The second problem was that the ADCP was dragged from its deployment location and flipped upside down in May 2006, perhaps by a barge moving through the area or being snagged by an anchor, resulting in a loss of about 1 month of data during May and June The quantity of data lost was reduced because the time between ADCP retrievals had been reduced from 12 weeks to 6 8 weeks. The third problem was that the CTDT could not be recovered in late summer, possibly due to it being covered by large debris. Another CTDT was deployed in late September

24 Results Tidal and seasonal variability is observed in the CTDT data collected at site SPB (fig. 13). Tidal variability in water depth appears as a thick band in figure 13. The increase in CTDT depth from November 2005 to July 2006 was due to placing the sensor in a slightly different location than the previous deployment and the possible gradual movement of the sonde towards deeper water because the anchor weight was insufficient. The temperature over the period of record shows a strong seasonal signal. During the winter, temperatures were smallest and temperature variability was relatively small because of a similarity in temperature between the freshwater inflow and the ocean water. During spring and early summer, heating from increased solar radiation and increasing temperature of the freshwater inflow resulted in greater temperatures and greater tidal variability of temperature in the bay. Salinity was relatively large and the tidal variability of salinity was relatively low during the fall, when freshwater input to the estuary was minimal. Salinity and salinity variability at the site reached a minimum during the large freshwater inflow in early January (greater than 10,000 m 3 /s). Salinity and the tidal variability in salinity returned shortly after the large flow pulse. Large tidal variability in salinity occurred in late spring when the freshwater inflow was large, relative to the low inflow during fall. From spring to summer, salinity increased and salinity variability decreased as inflow decreased. The SSC at the site responded primarily to the spring-neap tidal cycle and episodic wind-wave resuspension of shallow water sediments that advected to the site. SSC was greatest in January (table 6). SSC was higher during the more energetic spring tides than during the neap tides. The direct response of SSC to freshwater flow was negligible at this location. 24

25 Based on the limited, high-quality ADCP data available after March 7, 2006, the depth-averaged water velocity approached 1.5 m/s during spring tides (fig. 14). The maximum velocity in the water column reached 2 m/s near the surface (data not shown). Major wave events, induced by episodic (winter) and diurnal (summer) winds, occurred from the southwest and west, respectively, with wave periods between 3 and 5 seconds. Based on linear wave theory (Dean and Dalrymple, 1984), maximum significant wave heights of 0.6 m (4-second period) are capable of inducing near-bottom orbital velocities of 0.2 m/s in 6 m of water. The relative importance of wind waves and currents can been seen in late March (fig. 14). Prior to a large wind event, maximum SSC were 200 mg/l, while following the wind event, waves with 0.6 m significant wave height induced a SSC of more than 700 mg/l. The subsequent energetic spring tide, in the absence of strong wind waves, produced SSC up to 880 mg/l. Although freshwater inflow from the Delta delivers sediment from the Central Valley to the estuary, the direct effect of freshwater inflow on SSC for off-channel sites is minimal (fig. 15). Episodic winter winds that accompany Pacific storms have a greater effect on the site SSC due to the generation of wind waves and sediment resuspension in the shallows and transport to the site. Wind events in early December and early January doubled the SSC, relative to tidal currents alone (fig. 15), as suspended sediment was advected from the shallows of San Pablo Bay seaward past the site. High wind in late February coincided with high tide which probably limited the shear stress imparted by waves on the bottom and, thus, wind-wave resuspension. 25

26 The timing during the tidal cycle of peaks in SSC depends on the spring/neap tidal cycle and freshwater flow. Typically, peaks in SSC are associated with wind-wave induced resuspension in shallow areas of San Pablo Bay followed by advection of suspended sediment from shallower water rather than local resuspension at the site. Peak southwest winds (between dotted lines on fig. 16) coincide with ebb tide to create wind waves with significant wave heights exceeding 0.6 m (roughly at hour 36, fig. 16). These waves resuspended sediment in the landward portions of San Pablo Bay, which are significantly shallower than the instrument location. These sediments then were advected seaward during the ebb tide past the deployment location. SSC steadily increased through ebb tide, suggesting advection from landward regions as opposed to local resuspension. Peak SSC occurred after peak velocity, which supports advection as the main mechanism for increased SSC at the site. Thus, waves generated by the observed peak winds were too small to resuspend bottom sediment at the proposed Aquatic Transfer Facility site (SPB). The prior wave event (about hour 26 in fig. 16) did not result in either advection or increased SSC at the site because the bottom water velocities (and significant wave heights) and tidal excursion were much smaller. During spring tides when freshwater flow was relatively large, however, peak SSC occurred during floodtide rather than ebb tide. During March, April, and early May (the spring season, different from an energetic tide called a spring tide), freshwater flow from the Sacramento-San Joaquin River Delta was larger than any other time during the study period except early January (fig. 13). During periods of high flow, an estuarine turbidity maximum (ETM, a longitudinal maximum of SSC) is found in Carquinez Strait and tides can transport this ETM into the San Pablo Bay channel (Schoellhamer, 2001a). Synoptic cruise data indicate that the freshwater/saltwater interface and an ETM seaward of the interface were in the San Pablo Bay channel during spring 2006 (USGS, 2008). SSC in the turbidity maximum is much greater during high energy spring tides than during low energy neap tides (Schoellhamer, 2001a). Salinity at the study site increased rapidly early during flood tides (fig. 17). As 26

27 the salinity increases, SSC spikes for a short duration (fig. 17). Transport of the ETM from the channel in the floodtide direction (20 degrees clockwise from north) past site SPB probably caused the concurrent rapid salinity increase and SSC spike there. This spike is more apparent during the flood tide after the stronger ebb tide, perhaps because the larger ebb tide moves the channel ETM seaward of site SPB. When freshwater flow is smaller, the ETM is in eastern Carquinez Strait or Suisun Bay and tides would not transport it into San Pablo Bay. During neap tides, tidal energy and tidal excursion are smaller, the ETM contains less sediment and is less likely to move seaward of site SPB, so the SSC spike occurs during ebb rather than flood tide. During spring tides, peak SSC occurred during flood tide and during neap tides maximum SSC occurred during ebb tide during spring This caused the direction of residual suspended sediment flux [F] (eq. 2) to be in the flood tide direction during spring tides and the ebb tide direction during neap tides (fig. 18). During spring tides, the ebb tides move the channel ETM seaward of site SPB so that on the subsequent flood tide some of the ETM moves past the site. During neap tides, decreased tidal energy decreases SSC in the channel and the ETM may have been landward of site SPB. No flood tide spikes in SSC were observed at site SPB during neap tides and [F] was of smaller magnitude and in the ebb direction. Transport of sediment from the channel ETM toward the mudflats on the northern and eastern shore of San Pablo Bay during spring tide provides a mechanism for sediment delivery to the mudflats to help sustain them. Point San Pablo, Various processes cause suspended-sediment concentration in San Pablo Bay to vary over time scales ranging from seconds to years. Turbulence, semidiurnal tides, diurnal tides, other tidal harmonics, lower frequency tidal cycles, wind waves, watershed inflow, and climatic variability cause SSC to vary with time. Lower frequency variability is more difficult to quantify because continuous 27

28 SSC time series are difficult to collect for a long duration (months) and analytical tools typically require complete series with no missing data. 28

29 The mean water year SSC at mid-depth and near-bottom at site PSP (fig. 1) decreased in the late 1990 s (figs. 19 and 20). The water depth at site PSP is 7.9 m MLLW. SSC data have been collected at site PSP from 1992 to present (2006) every 15 minutes using optical sensors at mid-depth and nearbottom (Buchanan and Lionberger, 2006) (fig. 21). From water years to , mean mid-depth SSC decreased from 82 to 40 mg/l and near-bottom SSC decreased from 102 to 62 mg/l. The most likely explanation of these decreases is decreased sediment supply (McKee and others, 2006). Other possible explanations of these decreases are an increase in an in-bay sink, such as benthic filtration, or an increase in exchange with the less turbid Pacific Ocean. Monthly mean and median SSC for the mid-depth (table 7) and near-bottom (table 8) sensors show the previously discussed seasonal variation with greatest concentrations in winter and spring and smallest concentrations in autumn. Schoellhamer (2002) used singular spectrum analysis for time series with missing data (SSAM) to determine the contributions that various physical processes make to the variance of SSC. This analysis was done with data collected every 15 minutes from mid-depth at site PSP from 1992 to Physical processes that controlled SSC and their contribution to the total variance of SSC were (1) diurnal, semidiurnal, and other higher frequency tidal constituents (24 percent); (2) semimonthly tidal cycles (21 percent); (3) monthly tidal cycles (19 percent); (4) semiannual tidal cycles (12 percent); and (5) annual pulses of sediment caused by freshwater inflow, deposition, and subsequent wind-wave resuspension (13 percent). 89 percent of the total variance was explained and subtidal variability (65 percent) was greater than tidal variability (24 percent). 29

30 This analysis was repeated for this report using mid-depth and near-bottom data from 1992 to 2004 (fig. 21). Details of SSAM are described by Schoellhamer (2001b) and details of the specific method used here are described by Schoellhamer (2002). SSAM essentially is a principal components analysis in the time domain that extracts information from short and noisy time series with missing data without prior knowledge of the dynamics affecting the time series (Vautard and others, 1992; Dettinger and others, 1995; Schoellhamer, 2001b). The result is a set of reconstructed components that account for a known fraction of the original time series. The reconstructed components tend to be periodic and can be associated with physical forcing, such as different tidal periods or seasonal variability. Doubling the length of the mid-depth time series data from to produced results similar to the results of Schoellhamer (2002). Physical processes that controlled mid-depth SSC and their contribution to the total variance of mid-depth SSC were (1) diurnal, semidiurnal, and other higher frequency tidal constituents (28 percent); (2) semimonthly tidal cycles (24 percent); (3) monthly tidal cycles (7 percent); (4) semiannual tidal cycles (10 percent); and (5) annual pulses of sediment caused by freshwater inflow, deposition, and subsequent wind-wave resuspension (12 percent). 79 percent of the total variance was explained and again subtidal variability (51 percent) was greater than tidal variability (28 percent). Analysis of the near-bottom SSC at site PSP measured from 1992 to 2004 also produced similar results. Physical processes that controlled near-bottom SSC and their contribution to the total variance of near-bottom SSC were (1) diurnal, semidiurnal, and other higher frequency tidal constituents (31 percent); (2) semimonthly tidal cycles (15 percent); (3) monthly tidal cycles (10 percent); (4) semiannual tidal cycles (3 percent); and (5) annual pulses of sediment caused by freshwater inflow, deposition, and subsequent wind-wave resuspension (12 percent). 71 percent of the total variance was explained and subtidal variability (40 percent) was greater than tidal variability (31 percent). 30

31 Overall, SSC variability that could be attributed to diurnal, semidiurnal, and other higher frequency tidal constituents only was about 30 percent of the total SSC variance. Recognizable variability at longer (subtidal) time scales accounted for about percent of the total SSC variability overall, while noise accounted for the remaining (20- to 30-percent) variance. Processes at subtidal time scales accounted for more variance of SSC than processes at tidal time scales because sediment accumulated in the water column and the supply of easily erodible bed sediment increased during periods of increased subtidal energy. Sediment tended to accumulate in the water column during periods of stronger tides or wind because the duration of slack water was on the order of minutes in San Pablo Bay and, thus, limited deposition. For example, suspended sediment accumulates in the water column as a spring tide is approached and slowly deposits as a neap tide is approached (fig. 14). During a tidal cycle, the exchange of sediment between the water column and bed by way of deposition and resuspension, the supply of easily erodible bed sediment, and SSC increase with the subtidal energy. In addition, the supply of erodible sediment that experiences wind-wave resuspension in shallow water varies seasonally (Conomos and Peterson, 1977; Krone, 1979; Nichols and Thompson, 1985). Comparison of the effect of dredging operations and natural process on SSC at Point San Pablo Site PSP is 4.9 km south of the SF10 dredged material disposal site. This distance is less than a tidal excursion (the distance water moves during a flood or ebb tide), which is about km or the length scale of San Pablo Bay. Dredge material disposal would increase SSC at the disposal site. To determine whether SSC far from the site increased during dredging operations, Schoellhamer (2002) analyzed dredge disposal volumes and SSC data from Point San Pablo from to compare the basin-scale effect of dredging operations and natural estuarine processes. 31

32 Twelve periods of data were selected for analysis. Data were chosen from nondredging years to compare with years when dredging operations occurred. Data collected during 6 years were used ( ); 3 years with dredging operations and 3 years without. Two time periods, spring and summer, from each of the 6 years were analyzed to make a total of 12 time periods. The dates for analysis were the dates of dredging operations in spring 1997 (May 1 22) and summer 1995 (July 26 August 27). One exception was that the dates of dredging operations in 1993 (July 25 August 7) were used for the summer 1993 period. Dates from dredging years were used in nondredging years to attempt to reduce the effect of any seasonal process that could mask the effect of dredging operations. The SSC data were compared to dredging volume, Julian day, and hydrodynamic and meteorological variables that could affect SSC. Kendall s τ, Spearman s ρ, and weighted (by the fraction of valid data in each period) Spearman s ρ correlation coefficients (Conover, 1980; Helsel and Hirsch, 1992) of the variables indicated which variables were correlated significantly with SSC (table 9). Wind-wave resuspension had the greatest effect on SSC because median water-surface elevation was the primary factor affecting mid-depth SSC. Greater depths inhibit wind-wave resuspension of bottom sediment and indicate greater influence of less turbid water from Central Bay. Seasonal variability in the supply of erodible sediment is the primary factor affecting near-bottom SSC. Dredging volume and SSC at Point San Pablo were not correlated significantly at either mid depth or near bottom. Natural physical processes in San Pablo Bay are more areally extensive, of equal or longer duration, and as frequent as dredging operations (when occurring) and they affect SSC at the tidal time scale. Therefore, natural processes control SSC at Point San Pablo even when dredging operations are occurring (Schoellhamer, 2002). 32

33 Summary and Conclusions A conceptual model of sediment transport in San Pablo Bay was presented by Krone (1979). Sediment enters San Pablo Bay during large winter and spring flows from the Central Valley of California through Carquinez Strait. Wind waves in spring and summer resuspend deposited sediment and tidal currents transport this sediment. Autumn has the lowest SSC because wind waves are small and fine sediments have been winnowed from the bed, which is less erodible. There are several sources of sediment to San Pablo Bay (table 3). The largest source is sediment supply from Carquinez Strait (0.76 Mt/yr). Other sources in decreasing size are sediment supply from local tributary streams (0.28 Mt/yr), net erosion of the bottom of San Pablo Bay (0.45 Mt/yr), and net import of dredged material (0.04 Mt/yr). Deposition on tidal marsh adjacent to San Pablo Bay is a small sediment sink (0.08 Mt/yr). Conservation of mass was used to estimate that average annual sediment flux from San Pablo Bay seaward into Central Bay is 1.45 Mt/yr. San Pablo Bay has complex interactions with its tributary streams, which generally act as sediment traps. Barotropic convergence traps sediment and other constituents in the Napa/Sonoma Marsh (Warner and others, 2003). Baroclinic convergence traps sediment in Mare Island Strait where very large deposition has occurred historically (Warner and others, 2002). Tidally oscillating sediment masses near the mouths of the Petaluma River and Sonoma Creek contain the largest suspended sediment concentrations (SSC) measured in San Francisco Bay and create estuarine turbidity maxima (Ganju and others, 2004). 33

34 Several observations of sediment transport in San Pablo Bay generally corroborate the conceptual model of sediment transport first presented by Krone (1979). At channel marker 1 and in the vicinity of the proposed Aquatic Transfer Facility, freshwater flow pulses from the Central Valley have little effect on SSC. Greater erodibility is observed in winter than in summer. Tidal currents resuspend bottom sediment and SSC is greater on spring tides than on neap tides. Typically, wind-wave resuspension in shallower water and transport to the sites by ebb tidal currents account for observed SSC peaks. Residual suspended sediment flux is in the ebb direction. During spring tides when freshwater flow is relatively large, however, peak SSC occurs during flood tide. In this case, an estuarine turbidity maximum (ETM) moves into the San Pablo Bay channel and during the subsequent flood tide some of the ETM moves onto the San Pablo Bay shallows, increasing SSC. Residual sediment flux is in the flood direction. A 12-year continuous record of SSC at site Point San Pablo (PSP) shows variability at semimonthly (spring/neap), monthly, and semiannual tidal cycles in addition to the annual cycle of sediment supply and wind-wave resuspension. In addition, SSC during water years was about one-half the value during water years , probably due to decreased sediment supply from the Central Valley (McKee and others, 2006). Comparison of SSC at PSP and the volume of dredged material disposed nearby found no significant correlation (Schoellhamer, 2002). Natural physical processes in San Pablo Bay are more areally extensive, of equal or longer duration, and as frequent as dredging operations (when occurring) and they affect SSC at the tidal time scale. Therefore, natural processes control SSC at PSP even during dredging operations. 34

35 References Cited Buchanan, P.A., and Lionberger, M.A., 2006, Summary of suspended-sediment concentration data in San Francisco Bay, California, water year 2004: U.S. Geological Survey Data-Series Report 226, Burau, J.R., Simpson, M.R., and Cheng, R.T., 1993, Tidal and residual currents measured by an acoustic Doppler current profiler at the west end of Carquinez Strait, San Francisco Bay, California, March to November 1988: U.S. Geological Survey Water-Resources Investigations Report , 79 p. Cheng, R.T. and Gartner, J.W., 1984, Tides, tidal and residual currents in San Francisco Bay, California Results of measurements, : U.S. Geological Survey Water-Resources Investigations Report , 72 p. Conomos, T.J. and Peterson, D.H., 1977, Suspended-particle transport and circulation in San Francisco Bay, an overview: New York, Academic Press. Estuarine Processes, v. 2, p Conover, W.J., 1980, Practical nonparametric statistics: New York, John Wiley and Sons, 2 nd ed. Crimaldi, J.P., Thompson, J.K., Rosman, J.H., Lowe, R.J., and Koseff., J.R., 2002, Hydrodynamics of larval settlement: The influence of turbulent stress events at potential recruitment sites: Limnology and Oceanography, v. 47, no. 4, p

36 Dean, R.G., and Dalrymple, R.A., 1984, Water wave mechanics for engineers and scientists: Prentice- Hall, Englewood Cliffs, New Jersey, 353 p. Dettinger, M.D., Ghil, M., Strong, C.M., Weibel, W., and Yiou, P., 1995, Software expedites singularspectrum analysis of noisy time series: EOS, v. 76, no. 2, p. 12, 14, and 21. Dyer, K.R., 1974, The salt balance in stratified estuaries: Estuarine and Coastal Marine Science, v. 2, p Flick, R.E., Murray, J.F., and Ewing, L.C., 2003, Trends in United States tidal datum statistics and tide range: Journal of Waterway, Port, Coastal and Ocean Engineering, v. 129, no. 4, p Ganju, N.K. and Schoellhamer, D.H., 2006, Annual sediment flux estimates in a tidal strait using surrogate measurements: Estuarine, Coastal, and Shelf Science, v. 69, p Ganju, N.K., Schoellhamer, D.H., Warner, J.C., Barad, M.F., and Schladow, S.G., 2004, Tidal oscillation of sediment between a river and a bay: a conceptual model: Estuarine, Coastal, and Shelf Science, v. 60, no. 1, p Glysson, D.G., 1987, Sediment-transport curves: U.S. Geological Survey Open-File Report , 47 p. 36

37 Goals Project, 1999, Baylands ccosystem habitat goals, A report of habitat recommendations prepared by the San Francisco Bay Area Wetlands Ecosystem Goals Project: U.S. Environmental Protection Agency, San Francisco, Calif./S.F. Bay Regional Water Quality Control Board, Oakland, Calif. Helsel, D.R., and Hirsch, R.M., 1992, Statistical methods in water resources: Studies in Environmental Science, v. 49, Elsevier, New York. Jaffe, B. E., Smith, R. E., and Foxgrover, A., 2007, Anthropogenic influence on sedimentation and intertidal mudflat change in San Pablo Bay, California: 1856 to 1983: Estuarine, Coastal and Shelf Science, doi: /j.ecss Kineke, G.C., and Sternberg, R.W., 1989, The effect of particle settling velocity on computed suspended sediment concentration profiles: Marine Geology, v. 90, p Krank, K. and Milligan, T.G., 1992, Characteristics of suspended particles at an 11-hour anchor station in San Francisco Bay, California: Journal of Geophysical Research, v. 97, no. C7, p Krone, R.B., 1960, Silt transport studies utilizing radioisotopes: Hydraulic Engineering Laboratory and Sanitary Engineering Research Laboratory, Third Annual Progress Report, University of California, Berkeley, California, 52 p. Krone, R.B., 1979, Sedimentation in the San Francisco Bay system, In Conomos, T.J. (ed.), San Francisco Bay: The Urbanized Estuary. Pacific Division of the American Association for the Advancement of Science, San Francisco, California, p

38 Linville, R.G., Luoma, S.N., Cutter, L., and Cutter, G.A., 2002, Increased selenium threat as a result of invasion of the exotic bivalve Potamocurbula amurensis into the San Francisco Bay-Delta: Aquatic Toxicology, v. 57, no. 1 2, p McKee, L., Ganju, N.K., and Schoellhamer, D.H., 2006, Estimates of suspended sediment entering San Francisco Bay from the Sacramento and San Joaquin Delta, San Francisco Bay, California: Journal of Hydrology, v. 323, p Monismith, S., Burau, J.R., and Stacey, M., 1996, Stratification dynamics and gravitational circulation in northern San Francisco Bay, In Hollibaugh, J.T., (ed.), San Francisco Bay: The Ecosystem. Pacific Division of the American Association for the Advancement of Science, San Francisco, p Nichols, F.H. and Thompson, J.K., 1985, Time scales of change in the San Francisco Bay benthos: Hydrobiologia, v. 192, p Porterfield, G., 1980, Sediment transport of streams tributary to San Francisco, San Pablo, and Suisun Bays, California, : U.S. Geological Survey Water-Resources Investigations Report 80 64, 91 p. Poulton, V.K., Lovvorn, J.R., and Takekawa, J.Y., 2004, Spatial and overwinter changes in clam populations of San Pablo Bay, a semiarid estuary with highly variable freshwater inflow: Estuarine, Coastal and Shelf Science, v. 59, p

39 Ruhl, C.A., Schoellhamer, D.H., Stumpf, R.P., and Lindsay, C.L., 2001, Combined use of remote sensing and continuous monitoring to analyse the variability of suspended-sediment concentrations in San Francisco Bay, California: Estuarine, Coastal, and Shelf Science, v. 53, p Schoellhamer, D.H., 2001a, Influence of salinity, bottom topography, and tides on locations of estuarine turbidity maxima in northern San Francisco Bay, In McAnally, W.H., Mehta, A.J. (eds.), Coastal and Estuarine Fine Sediment Transport Processes: Elsevier Science B.V., p Schoellhamer, D.H., 2001b, Singular spectrum analysis for time series with missing data: Geophysical Research Letters, v. 28, no. 16, p URL: Schoellhamer, D.H., 2002, Comparison of basin-wide effect of dredging and natural estuarine processes on suspended-sediment concentration: Estuaries, v. 25, no. 3, p Schoellhamer, D.H., and Burau, J.R., 1998, Summary of findings about circulation and the estuarine turbidity maximum in Suisun Bay, California: U.S. Geological Survey Fact Sheet FS , 6 p. Smith, B.J., 1963, Sedimentation in the San Francisco Bay System: Proceedings of the Second Federal Interagency Sedimentation Conference, Jackson, Miss., p Swanson, K., Shellenbarger, G.G., Schoellhamer, D.H., Ganju, N.K., Athearn, N., and Buchanan, P.A., 2003, Desalinization, erosion, and tidal changes following the breaching of Napa salt pond 3: Proceedings of the 6th biennial State-of-the-Estuary Conference, Oakland, California, October 21 23, 2003, p

40 United States Geological Survey, 2008, Water quality of San Francisco Bay, Vautard, R., Yiou, P., and Ghil, M., 1992, Singular-spectrum analysis A toolkit for short, noisy, chaotic signals: Physica D, v. 58, p Warner, J.C., Schoellhamer, D.H., Burau, J., and Schladow, G.S., 2002, Effects of tidal current phase at the junction of two straits: Continental Shelf Research, v. 22, p Warner, J.C., Schoellhamer, D.H., and Schladow, G.S., 2003, Tidal truncation and barotropic convergence in a channel network tidally driven from opposing entrances: Estuarine, Coastal and Shelf Science, v. 56, p

41 Figure 1. San Francisco Estuary and San Pablo Bay. 41

42 Figure 2. Instantaneous (Q) and tidally averaged discharge ([Q]), velocity-weighted suspended-sediment concentration (SSC u ), and flux components in Carquinez Strait. Positive values indicate downstream (ebb) transport; negative values indicate upstream (flood) transport. From Ganju and Schoellhamer (2006). 42

43 Figure 3. Barotropic convergence zone in the Napa/Sonoma Marsh. Directions of flooding currents were determined from the instrument deployment described by Warner and others (2003). 43

44 Figure 4. Junction of Mare Island and Carquinez Straits showing the development of the local salinity minimum (Warner and others, 2002). Darker shading denotes saltier water. 44

45 Figure 5. Time-series of velocity from site Pet (1), suspended-sediment concentrations from site Pet (2), site CM9 (3), site PSP (4). Arrows do not indicate the same parcel of sediment advecting from site to site, but rather the general motion of suspended sediment between the deposits. 45

46 Figure 6. Time-series of velocity from sites SNS and Pablo (1), suspended-sediment concentrations from site SNS (2), site Pablo (3), sites PSP and Ben (4).. 46

47 Figure 7. Time-series of water level at site CM9 (A), wind speed at site Novato (B), and suspended-sediment concentrations (SSC) from sites CM9 and Pet (3), November 4 to November 21,

48 Figure 8. Time-series of Delta outflow, wind speed, and suspended-sediment concentration from the lower sensor at Carquinez Bridge (CAR), Channel marker 1 (CM1), and the lower sensor at Point San Pablo (PSP). Delta outflow data were obtained from 48

49 Figure 9. Time-series of Delta outflow, daily averaged wind speed, and daily averaged suspended-sediment concentrations from the lower sensor at Carquinez Bridge (CAR), Channel marker 1 (CM1), and the lower sensor at Point San Pablo (PSP). Delta outflow data were obtained from 49

50 Figure 10. Time-series of wind speed at Carneros, water level at Channel marker 1 (CM1), salinity at CM1, and suspendedsediment concentration (SSC). 50

51 Figure 11. Details of conductivity, temperature, depth, and turbidity (CTDT) sonde mooring. 51

52 Figure 12. Details of acoustic Doppler current profiler (ADCP) mooring. 52

53 Figure 13. Delta outflow, depth, water temperature, salinity, and suspended sediment concentration (SSC) from the nearbottom sonde at site SPB. Delta outflow data were obtained from 53

54 Figure 14. ADCP depth, salinity, mean (depth-averaged) water velocity, wind speed at Carneros, significant wave height, and suspended-sediment concentration (SSC) at site SPB. 54

55 Figure 15. Delta outflow, wind speed at Carneros, and suspended-sediment concentration (SSC) at site SPB. Delta outflow data were obtained from 55

56 Figure 16. Three-day record of depth, mean water velocity, wind speed at Carneros, significant wave height, and suspendedsediment concentration (SSC) at site SPB. Vertical dashed lines indicate the period of peak southwest wind. 56

57 Figure 17. Current speed, current direction, salinity, and suspended-sediment concentration (SSC) at the San Pablo Bay study site SPB. Current direction is clockwise from north. Flood tide is directed slightly clockwise from north (20 degrees). 57

58 Figure 18. Water depth and residual suspended sediment flux [F] at the San Pablo Bay study site SPB. [F] is shown as a vector with north up. A daily subsample of [F] is shown for clarity. Flood tide is directed slightly clockwise from north (20 degrees). 58

59 . SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER WATER YEAR Figure 19. Mean mid-depth suspended-sediment concentration at Point San Pablo, water years

60 SUSPENDED-SEDIMENT CONCENTRATION, IN MILLIGRAMS PER LITER WATER YEAR Figure 20. Mean near-bottom suspended-sediment concentration at Point San Pablo, water years

61 Figure 21. Suspended-sediment concentrations at Point San Pablo, mid-depth and near-bottom,