Upper Manistee River Instream Fish Habitat Assessment

Transcription

1 1 Upper Manistee River Instream Fish Habitat Assessment Michigan Trout Unlimited January 216 Kristin Thomas Dr. Bryan Burroughs

2 2 Table of Contents INTRODUCTION... 4 Table 1. Michigan stream and river temperature classification criteria Figure 1. Map of the Upper Manistee River DATA EXAMPLES... 5 Figure 2. Hypothetical bedform composition data for a healthy balanced river... 7 Figure 3. Hypothetical substrate composition data for a healthy rive) Figure 4. Hypothetical in-stream habitat data for a river with good diverse habitat METHODS... 9 Table 2. Bedform delineation explanation Table 3. Substrate classes used to denote substrate composition Table 4. Descriptions of the 11 original Upper Manistee River and Portage Creek mapping sites Figure 5. Upper Manistee River Watershed Substrate Composition Figure 6. Upper Manistee River Watershed bedform structure Figure 7. Upper Manistee River Watershed in-stream fish cover Table 5. Description of the five Upper Manistee River segments and two Portage Creek segments RESULTS AND DISCUSSION UPPER MANISTEE RIVER ANALYSIS: WHOLE RIVER Figure 9. Upper Manistee River bedform delineation, bottom substrate, and in-stream fish cover Figure 1. Portage Creek bedform delineation, bottom substrate, and in-stream fish cover UPPER MANISTEE RIVER ANALYSIS: BY SEGMENT Bedform Structure Figure12. Bedform structure of segments in the Upper Manistee River In-stream Habitat Availability Substrate Composition Figure 14. Upper Manistee River substrate composition by segment Figure 15. Upper Manistee River fine and hard substrate composition by segment PORTAGE CREEK ANALYSIS: BY SEGMENT Bedform Structure In-stream Habitat Availability Substrate Composition Recommendations and Management Actions LITERATURE CITED... 34

3 3 Purpose & Context Many coldwater streams in Michigan, including the Upper Manistee River, lack comprehensive data on instream fish habitat conditions. Research has been done to verify that temperature, catchment size, and 9% exceedance flow have a substantial impact on fish community (Zorn et al. 29, Zorn and Wiley 24). However, at this time there is not research available which relates the amount, quality, or spatial distribution of in-stream habitat to fisheries population dynamics (density or size structure). Some work has been done to determine if the addition of woody debris has positive impacts on fisheries populations (Roni and Quinn 21, Bryant 1983), but has not looked at how much wood is needed or optimal. It is our long-term intent to develop paired habitat and fisheries data sets that can be used to statistically determine the degree to which in-stream habitat, substrate, and bedforms shape fisheries populations in Michigan. The ultimate goal of having that scientific insight, would be to assess a stream and fishery and be able to confidently diagnose the limiting factors and ensure that actions taken to improve fisheries will result in those benefits being realized. With that in mind, fisheries habitat data was collected, summarized, and discussed in the context of prioritizing restoration and protection efforts in the Upper Manistee River. An emphasis was placed on coldwater fisheries habitat. This methodology was used because it provides a comprehensive habitat inventory for the entire river, or a segment of river, in contrast to a small random subsample that may not accurately depict the variability of habitats that truly represent a river s current conditions. The Upper Manistee River was surveyed from Mancelona to Sharon (45 miles) in 214. This report summarizes the data collected during this survey. It is important to note, that currently, rigorous statistical relationships between instream fish habitats and fish populations are not available. This means that we are not yet able to place these results for the Upper Manistee River in a broader statistical context for identifying and justifying priority improvements to target. At this point in time, we must interpret these results in limited context with the other rivers we have thus surveyed, using the professional or expert judgments of those intimately familiar with our streams geomorphology and fish populations, and with experience in the practice of stream enhancement techniques and costs. With that said, this report provides summaries of the results of the survey, and interpretations and recommendations of it that represent TU staff s best professional judgment. This platform will be best put to use through engagement of other partners and practitioners for review and interpretation, to the end of us all doing the best we can to ensure the improvement and protection of the Upper Manistee River. If you review this report and would like to provide further comments, discussion, alternate interpretations or recommendations for improvement, we welcome all feedback and are available to facilitate further discussion.

4 4 Introduction The Upper Manistee River is a valued coldwater fishery located in northern Lower Michigan. The Upper Manistee River watershed drains 59 square miles; the mainstem is approximately 78 miles long. The Upper Manistee River is a cold small river from Mancelona to Sharon. At Sharon it transitions to a coldtransitional large river, one of the rarest river types in Michigan (Table 1). Table 1. Michigan stream and river temperature classification criteria. Temperature ranges are based on predicted mean July water temperature ( F). These classification are the base for protection limits from large quantity water withdrawals under MI statute (Part 327). Classification Temperature Range Cold <63.5 F Cold-Transitional F Cool F Warm >69.8 F Prior to this survey there was limited current fish habitat data available for the Upper Manistee River. Some road stream crossing and habitat data are available from Conservation Resource Alliance and the DNR. This is great data; however, it does not focus on the status of instream fish habitat conditions in the entire river. The purpose of this survey was to catalog in-stream habitat to determine how it may be limiting the coldwater fishery. It is important to note that fish habitat data is only one of the tools used to identify factors that may be limiting a coldwater fishery, albeit a critical one in which data is typically lacking. Habitat mapping differs from many types of habitat monitoring in that fish habitat is surveyed in the entire river, or an entire sub-section of a watershed. It serves as more of a census than a survey. The survey included; delineating the river channel into bedform types (run, riffle, or pool), recording the length, location, and width of each bedform unit; and the characterization of the amounts of in-stream fish cover (aquatic vegetation, woody debris, and deep water) and streambed substrate composition in each bedform unit. The full methodology is explained and supported in a separate manual, found at, Each of these variables is important to the health of a coldwater fish community. A variety of bedform structures are needed for a healthy fishery. Each species of fish, at different stages of their life, have specific needs for survival, growth and feeding, and reproduction, and it takes a variety of habitats to provide for all of those unique needs. For example, riffles with coarse substrate are used for spawning and are critical habitat for numerous species of macroinvertebrates, which provide food for trout. Bottom substrate heterogeneity is also important in providing a variety of food sources. A variety of substrate types (gravel, cobble, silt, wood, leaf packs, etc.) provide habitat for a diverse macroinvertebrate community and thus a variety of food sources for coldwater fish. Areas that can hold and hide fish are also important. Woody debris, deep water, and aquatic vegetation are examples of fish habitats which provide cover. Trout and other fish can seek refuge from predators in these areas.

5 5 In 214 approximately 45 miles of the Upper Manistee River were mapped. In 215, approximately 8 miles of Portage Creek, a tributary of the Upper Manistee River, were mapped (Figure 1). Habitat mapping data collected on the Upper Manistee River in 214 and Portage Creek in 215 is summarized in this report. Trends in bedform composition, substrate composition, and fish habitat structure were compared in five segments of the Upper Manistee River and two segments of Portage Creek. Direction of Flow Figure 1. Map of the Upper Manistee River. The mainstem of River was mapped from Mancelona to Sharon. Portage Creek was mapped from Euclid Avenue to the Manistee River. Data Examples As discussed in the Purpose & Context section, we do not currently possess well-developed quantitative relationships between instream fish habitat variables and stream fish populations. However, we do have confidence in several general ecological principles. 1.) Habitat heterogeneity and diversity is desired. It provides for habitats to suit many macroinvertebrate and fish species and their various life stages, generally leading to healthy populations, diverse fish communities, and ecosystem resiliency. In contrast, homogeneity of habitats, while possibly benefiting a few select species, generally leads to less productive and resilient fish communities. 2.) Stream fish such as trout, unless prevented from migrating throughout a river system by impassable barriers, will move considerable distances to reach unique habitats they needed for different purposes. If connectivity between river segments exist, each segment need not offer

6 6 all habitat elements in ideal levels, rivers can form mosaics of different habitats that taken and functioning as a whole provide all the necessary elements. 3.) Trout, salmon and steelhead are lithophilic spawners, meaning they require gravel substrates of the right size ranges, with specific water velocities to reproduce. We do not well understand the exact amounts of this habitat in a stream that are required to ensure maximum spawning potential and success for a given population, but these habitats are essential. 4.) Wood material is critically important in Michigan streams, for influencing channel form, localized substrates, nutrient cycling, substrates for macroinvertebrates, and cover for fish. We do not yet understand how much wood is optimal. Is more wood always better for trout, or is it only better to a certain point, with no real benefit after that? We do not yet understand finetuned wood dynamics, but do know it is a critical component to healthy stream fisheries in the Midwest. 5.) Deep water, defined here as >2.5 ft. deep, provides security and comfort to many species of fish in streams, and for large sizes of trout. Very wide and shallow habitats can be productive habitat for small fish and juvenile trout, but generally, larger sizes of stream trout require presence of deep water and other forms of cover. 6.) Moderate slopes or gradients of streams tend to lead to the formation of more riffle and pool bedforms, interspersed with runs. As slopes decrease, riffle and pools become less frequent, and bedforms are dominated by runs. When run bedforms are dominant, it becomes essential that habitat complexity and diversity is accomplished by other habitat elements such as deep water, wood material, and aquatic vegetation. 7.) We are not yet able to confidently state how much sand substrate is deleterious to a trout population. The negative impact of sand to a trout population generally, has been well documented. But exact impacts to a population will be dependent on many other variables, including the abundance and distribution of other forms of critical habitat (which may or may not co-vary with sand). So, we examine the results of instream fish habitat assessments through these very general principles, looking first for clear and obvious deficiencies or imbalances of critical habitats, and secondarily for potential elements that could be optimized further in specific locations. The following are hypothetical data scenarios to familiarize the reader with these concepts and the data summaries to follow. A healthy stream will have diverse bedform structure with ample run, riffle, and pool habitat. The river will not be dominated by one bedform type (Figure 2). River A has a good balance of bedform types, whereas River B is dominated by run habitat with little riffle or pool habitat available. The dominance of run habitat in river B may indicate a problem.

7 7 A) B) Figure 2. Hypothetical bedform composition data for a healthy balanced river (A) and a river with limited bedform heterogeneity (B). A variety of substrate types are also present in a healthy river. It is especially important that fine sediments (sand and silt) do not dominate a river bottom. Erosion is a major source of pollution to our waterways, an overabundance of fine sediment may be a sign that there is an erosion problem in the watershed, or a legacy of past sedimentation that has not been flushed out of the system. A healthy river will have a balance of substrate types (Figure 3). River A has a good balance of fine and hard substrate; whereas river B is dominated by silt and sand with little hard substrate present.

8 8 A) B) Figure 3. Hypothetical substrate composition data for a healthy river (A), and a river with excess fine sediment (B). In-stream habitat diversity, or fish cover is also an important portion of what makes a stream ideal for coldwater fish. Fish need a variety of places to seek cover from predators including aquatic vegetation, woody debris, and deep water. River A has abundant, diverse in-stream fish habitat (8%); whereas, river B has sparse in-stream habitat available (25%) (Figure 4).

9 9 A) B) Figure 4. Hypothetical in-stream habitat data for a river with good diverse habitat (A), and a river deficient in-stream habitat (B). Graph A in Figures 2-4 depict a healthy river, ideally each river mapped will have data similar to that generally seen in the A graphs. Graph B in Figures 2-4 depict issues which may be indicative of a limitation to the coldwater fishery. When we see data similar to that in the B graphs restoration or enhancement may be needed, and more in-depth analysis and discussion is appropriate. Methods Methodological details for this instream fish habitat assessment can be found in full detail in report form, at:

10 1 This survey was conducted by summer interns working for Michigan Trout Unlimited. The interns were trained in habitat mapping methods by Michigan Trout Unlimited (MITU) Aquatic Ecologist Kristin Thomas. All mapping was completed during average or low flow conditions. It is important that habitat is not mapped during times of high flow because high flow can make it difficult to distinguish bedform delineations. Mapping on the Upper Manistee was completed in June of 214. Mapping on Portage Creek was completed in July of 215. Training included instruction on how to determine bedform delineation, substrate classification, and practice visually estimating percent of streambed. Stream diagrams were used to practice estimating the percent of streambed occupied by substrate types and fish cover. Volunteers estimated substrate composition and fish cover for each diagram. A key with a grid and actual percentages were then provided. This exercise was used to help the member visually estimate percent of stream bottom. Bedform delineation and qualitative observations were derived through independent visual observations and evaluations. Bedform delineation involved the categorization of the stream into bedforms (run, riffle, pool, rapid, as defined in Table 2). The length and widths (top and bottom) of each bedform section were measured. Latitude and longitudes were recorded at the top and bottom of each bedform section using a handheld GPS. Measurements of bedform lengths and widths were made with a Nikon Laser Rangefinder (+/-.5 yard accuracy) or a tape measure. Quantitative streambed substrate composition measurements were made through visual estimation. The percent area of each bedform segment occupied by clay, silt, sand, gravel, cobble, or boulder was estimated visually. Substrate classification followed Wolman size classes for sand, gravel (all sizes combined), and cobble (all sizes combined) (Table 3). The percent area of streambed in each bedform section covered by woody debris, aquatic vegetation and deep water (>2.5 ft.) was also visually estimated. The amount of wood, vegetation, and deep water was expressed as a percent of streambed area (5% increments). The maximum depth present in each bedform section was also recorded. In cases were maximum depth could not be measured; maximum depth was listed as greater than 4 feet. Table 2. Bedform delineation explanation. Bedform Description Run Riffle Fast or slow current, unbroken water, average depth. Swift current, turbulent broken water, shallower than average depth. Pool Slow or no current, unbroken water. Generally about 1.5 times deeper than average depth. Rapid Waterfall Swift current, very turbulent, broken water. Large boulders or bedrock often breaking the surface. The majority of the stream flow over a ledge or cliff.

11 11 Table 3. Substrate classes used to denote substrate composition. Particle Description Clay Silt Sand Gravel Cobble Boulder Bedrock Very fine sticky texture. Easily forms ribbons when rolled in hand, generally reddish or gray in color. Very fine texture. Smooth, silky feel when handled. Crumbles readily when handled. Single sand grains are apparent. Rocks 1/16 to 2 ½ inches in diameter Rocks 2 ½ to 1 inches in diameter. Rocks greater than 1 inches in diameter. Solid rock surface, not the tops of boulders. The Upper Manistee River was originally divided into 11 habitat mapping sites, for the purpose of organizing field data collection. In most cases, access points dictated the beginning and end of each site. Habitat data for all of the mapped portions of the river were analyzed and then the 1 sites were grouped into 5 analysis segments. Portage Creek was originally divided into 3 sites, grouped in two analysis segments (Table 4). Segments were chosen based on commonalities in habitat conditions, and clear contrasts between them. Figures 5-7 below are provided to illustrate that the consolidation into 7 segments for analysis was based off similarities in instream habitat elements, and not arbitrary grouping that would obscure significant differences between the segments. Table 4. Descriptions of the 11 original Upper Manistee River and Portage Creek mapping sites. Shading indicates transition between 7 segments used in analysis. Site Name Site Description Segment Manistee 1 Mancelona to Deward Norway Segment 1 Manistee 2 Deward Norway to Deward Oxbow Segment 1 Manistee 3 Deward Oxbow to County Rd. 612 Segment 1 Manistee 4 County Rd. 612 to Loggers Landing Segment 2 Manistee 5 Loggers Landing to M-72 Segment 2 Manistee 6 M-72 to Hole in the Wall Segment 3 Manistee 7 Hole in the Wall to Yellow Trees Segment 3 Manistee 8 Yellow Trees to Lease M-35 Segment 4 Manistee 9 Lease M-35 to CCC Bridge Segment 5 Manistee 1 CCC Bridge to 4 Mile Bend Segment 5 Manistee 11 4 Mile Bend to Sharon Segment 5 Portage 1 Euclid Ave. to Kalkaska County Line Segment 1

12 Manistee 1 Manistee 2 Manistee 3 Manistee 4 Manistee 5 Manistee 6 Manistee 7 Manistee 8 Manistee 9 Manistee 1 Manistee 11 Portage 1 Portage 2 Portage 3 Percent of River Bottom Manistee 1 Manistee 2 Manistee 3 Manistee 4 Manistee 5 Manistee 6 Manistee 7 Manistee 8 Manistee 9 Manistee 1 Manistee 11 Portage 1 Portage 2 Portage 3 Percent of River Bottom Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat 12 Portage 2 Kalkaska County Line to Trout Trail Segment 1 Portage 3 Trout Trail to Manistee River Segment Upper Manistee Substrate Composition Hard Fine Figure 5. Upper Manistee River Watershed Substrate Composition. Fine silt and sand. Hard clay, gravel, cobble, and boulder. Red lines represent analysis segment divisions Upper Manistee Bedform Structure Pool Riffle Run Figure 6. Upper Manistee River Watershed bedform structure. Red lines represent analysis segment divisions.

13 Mansitee 1 Mansitee 2 Mansitee 3 Mansitee 4 Mansitee 5 Mansitee 6 Mansitee 7 Mansitee 8 Mansitee 9 Mansitee 1 Mansitee 11 Portage 1 Portage 2 Portage 3 Percent of River Bottom Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat 13 Upper Manistee In-stream Habitat Vegetation Wood Deep Figure 7. Upper Manistee River Watershed in-stream fish cover. Red lines represent analysis segment divisions. Table 5. Description of the five Upper Manistee River segments and two Portage Creek segments used for analysis. Segment Name Segment Description Segment Length (miles) Segment 1 Mancelona to County Rd Segment 2 County Rd. 612 to M Segment 3 M-72 to Yellow Trees 9.7 Segment 4 Yellow Trees to Lease M Segment 5 Lease M-35 to Sharon 11.5 Segment 1 Euclid Ave. to Trout Trail 5.5 Segment 2 Trout Trail to Manistee River 2.4

14 14 Segment 1 Segment 2 Segment 3 Segment 4 Segment 5 Figure 8. Map of the Upper Manistee River, showing the 5 main segments of the river related to distinct differences in instream fish habitat conditions. Boundary descriptions found in Table 5. Segment 1 Segment 2 Figure 9. Map of Portage Creek River, showing 2 main segments of the river related to distinct differences in instream fish habitat conditions. Boundry descriptions found in Table 5.

15 15 Habitat features for each segment are summarized (Table 6, Table 7). For all analyses, percent of total streambed was used. For example, to determine what percent of the Upper Manistee River is run, riffle, and pool the total area of run, riffle, and pool was calculated and then expressed as a percent of total streambed area. To calculate the area of each bedform section the mean bedform section width (top width + bottom width/2) was multiplied by bedform section length. Percent substrate and habitat was calculated by expressing the percent substrate or habitat as an area (i.e. (percent gravel/1)*bedform section area). The total area of sand, gravel, cobble etc. was then summed and expressed as a percent of total stream or segment area. Thus, each percent presented on a graph represents the proportion of total stream bed occupied by that in-stream habitat element as estimated for this study. The deepest point in each bedform section was also recorded. This allowed for the calculation of minimum width to depth ratio. We were unable to calculate width to depth ratio in the traditional format because we do not have a mean depth or bankfull width for each bedform section (width to depth ratio = bankfull width/mean depth). Therefore, we calculated minimum width to depth ratio = wetted width/maximum depth. This calculation results in a smaller number than a traditional width to depth ratio; thus, it is referred to as minimum width to depth ratio. In cases where maximum depth was listed as greater than 4 feet, 4 feet was used to calculate minimum width to depth ratio. Results and Discussion Table 6. Instream fish habitat summary data for the Upper Manistee River. Percentages and proportions are mean values for all bedform segments in the river as a whole and within each section. All Sections Mapped Segment 1 Segment 2 Segment 3 Segment 4 Segment 5 Total Length (ft.) 237,384 55,718 48,521 51,134 21,392 6,619 Width (ft.) Mean Range Percent Run Bedform Percent Riffle Bedform Percent Pool Bedform % Deep Water (>2.5 ft.) % Woody Debris % Aquatic Vegetation Total Section - % Clay Total Section - % Silt Total Section - % Sand Total Section - % Gravel Total Section - % Cobble Total Section -% Boulder

16 16 Table 7. Instream fish habitat summary data for the Portage Creek. Percentages and proportions are mean values for all bedform segments in the stream as a whole and within each section. All Sections Mapped Segment 1 Segment 2 Total Length (ft.) 41,627 28,923 12,74 Width (ft.) Mean Range Percent Run Bedform Percent Riffle Bedform Percent Pool Bedform % Deep Water (>2.5 ft.) % Woody Debris % Aquatic Vegetation Total Section - % Clay Total Section - % Silt Total Section - % Sand Total Section - % Gravel Total Section - % Cobble 1 2 Total Section -% Boulder Upper Manistee River Analysis: Whole River The Upper Manistee River is dominated by run habitat (92% in the mainstem, 98% in Portage Creek) (Table 6, Table 7, Figure 9, and Figure 1), but ranks moderate in percentage of run compared with other surveyed Michigan trout streams (Figure 11-A). The remaining bedform habitat is split between riffle (6%) and pool (2%) in the mainstem. In Portage Creek, there is no riffle habitat and only 2% pool (Table 7, Figure 1). The dominance of run habitat is also high when compared with other Michigan trout streams surveyed (Figure 11-A). In the Upper Manistee River, sand is the most common substrate (69%) followed by gravel (24%), with smaller amounts of silt and cobble (Table 6, Figure 1-B). Sand is dominant in Portage Creek accounting for 89% of the total substrate (Table 7, Figure 11-B). These two rivers have the highest proportion of sand of all 16 Michigan streams surveyed to date (Figure 11-B). While the level of sand in the Upper Manistee does rank high relative to other Michigan trout streams surveyed, the percent gravel is comparable to other rivers like the Little Manistee and Black Rivers, where sand is dominant, but the available gravel is known to produce larger levels of trout reproduction (Figure 11-B). Cumulative fish cover (wood, deep water and aquatic vegetation) for the Upper Manistee River was 75%, Portage Creek had 94% cumulative fish cover (Figure 11-D). These are the highest totals of fish cover among rivers surveyed (Figure 11-D). There was a moderate amount of wood habitat available in the Upper Manistee River (19%), Portage Creek had a high amount of wood (39%) (Table 6, Table 7, Figure 11-F). Deep water habitat was ample in both the Upper Manistee River (42%) and Portage Creek (25%) (Figure 11-E). Portage Creek had the highest percent of aquatic vegetation of

17 17 surveyed rivers (3%), the Upper Manistee had 14% aquatic vegetation, a moderate amount compared to other surveyed rivers (Figure 11-G). The Upper Manistee and Portage Creek do have higher percentages of fine substrate (predominantly sand) than most other analyzed streams in Michigan (Figure 11-B). When substrate types are grouped into hard or fine groupings, based on the ecological function (fine = sand and silt), the Upper Manistee River and Portage Creek have a high proportion of fine substrate as compared to other surveyed rivers, in fact Portage Creek had the highest percent fine recorded to date (Figure 11-C). To a large extent, the dominance of run habitat and sandy substrate in so many Michigan Rivers can be explained by geology and geomorphology. Most rivers in Michigan s Lower Peninsula, including the Upper Manistee and Portage Creek are low gradient streams which limits the amount of riffle that will naturally occur in the stream. However, even compared to other low gradient streams in Michigan the Upper Manistee and Portage Creek have a very limited quantity of riffle and pool habitat (Figure 11-A). These systems have very high levels of fish cover. It seems the clear limiting factors here are substrate and bedform related (Figure 11). This does not mean that in-stream habitat could not be improved to more ideal conditions, but it does not appear to be the clearest limiting factors for this river s trout fishery today. However, sediment and lack of bedform heterogeneity do appear to be the clearest deficiencies for physical habitat in the portions of the Upper Manistee River watershed surveyed. Out of all the trout streams we ve thus surveyed, the Upper Manistee River ranks in the lowest 4 for bedform heterogeneity and percent sand substrate. Data for the whole river is useful comparing to other rivers in the region and identifying clear deficiencies, such as fish cover abundance. However, data from analysis of specific segments will be used in the next section to identify areas of need and potential projects.

18 Percent of River Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat 18 A) Upper Manistee Bedform Composition Run Riffle Pool B) C) Upper Manistee Substrate Composition Clay Silt Sand Gravel Cobble Boulder Upper Manistee In-stream Habitat Deep Water Wood Aquatic Vegetation Figure 9. Upper Manistee River bedform delineation, bottom substrate, and in-stream fish cover.

19 Percent of River Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat 19 A) 1 Portage Creek Bedform Composition Run Riffle Pool Portage Creek Substrate Composition B) Clay Silt Sand Gravel Cobble Boulder C) Portage Creek In-stream Habitat Deep Water Wood Aquatic Vegetation Figure 1. Portage Creek bedform delineation, bottom substrate, and in-stream fish cover.

20 Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat Bedform Delineation Pool Riffle Run Figure 11-A. Proportions of bedforms in the 16 trout streams (surveyed by MITU) in Michigan, ordered by percent run bedform (black). Substrate Composition Boulder Cobble Gravel Sand Silt Clay Figure 11-B. Streambed substrate composition in the 16 trout streams (surveyed by MITU) in Michigan, ordered by percent sand.

21 Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat Substrate Composition - Hard & Fine Groups Hard Fine Figure 11-C. Hard and fine substrates composition in the 16 trout streams (surveyed by MITU) in Michigan, ordered by percent fine substrate Cumulative Fish Cover Figure 11-D. Cumulative percent area of in-stream fish cover in the 16 trout streams (surveyed by MITU) in Michigan, including deep water, wood debris and aquatic vegetation.

22 Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat Percent Deep Water (>2.5 ft) Figure 11-E. Percent area of deep water (>2.5 ft.) in the 16 trout streams (surveyed by MITU) in Michigan Percent Wood Debris Figure 11-F. Percent area of wood debris in the 16 trout streams (surveyed by MITU) in Michigan.

23 Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat Percent Aquatic Vegetation Figure 11-G. Percent area of aquatic vegetation in the 16 trout streams (surveyed by MITU) in Michigan. Upper Manistee River Analysis: By Segment The 11 habitat mapping sites in the Upper Manistee River were organized into 5 distinct segments for indepth habitat analysis. Segments were grouped based on distinct changes in river habitat to allow for analysis of similar sections of river. Segment 1 consists of sites 1-3. These sites were grouped because of their relatively high bedform heterogeneity and percent of hard substrate. Segment 2 consists of sites 4-5 and were grouped because of the relatively high abundance of run habitat and fine substrate compared to sites 1-3. Segment 3 is sites 6-7 and was offset from segment 2 because of increase in hard substrate and fish cover as compared to segment 2. Segment 4 is site 8 which was separated because of the relatively high percent fine substrate as compared to segments 3 and 5. Segment 5 is sites 9-11, where riffle habitat and hard substrate are more prevalent than in the adjacent segment (Table 4, Figures 5, 6, and 7). Bedform Structure In the Upper Manistee River as a whole there is limited riffle and pool habitat (Figure 12). Segment 1 is mostly run habitat, with a minimal amount of riffle and pool habitat (Figure 12). Segments 2 and 3 are almost entirely run habitat with a minimal amount of pool in segment 2. Segment 4 has slightly more pool and riffle than segments 2 and 3, but still is dominated by run. Segment 5 is unique in the Upper Manistee River in that it has the majority of the riffle habitat in the area surveyed (Figure 12). The riffle habitat in segment 5 should be assumed to be key critical spawning habitat for trout, and treated as key reproduction area by ensuring sedimentation does not impact this area in the future.

24 Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat Bedform Structure by Segment Segment 1 Segment 2 Segment 3 Segment 4 Segment 5 Pool Riffle Run Figure12. Bedform structure of segments in the Upper Manistee River. In-stream Habitat Availability The Upper Manistee River as a whole has ample in-stream fish habitat. All segments have over 5% cumulative fish habitat, which is relatively high (Figure 13, Figure 11-D). Segments 3 and 4 both have greater than 9% fish habitat (Figure 13). In these two segments, deep water accounts for a large portion of the habitat, however there is also ample wood and aquatic vegetation in these areas (Figure 13). Segments 1 and 2 have less deep water habitat than other segments, but still have ample fish habitat In-stream Habitat by Segment Vegetation Wood Deep 2 1 Segment 1 Segment 2 Segment 3 Segment 4 Segment 5 Figure 13. In-stream habitat structure in the Upper Manistee River.

25 25 Substrate Composition Sand is the most common substrate in all segments of the Upper Manistee River. Hard substrate (gravel and cobble) does not dominate in any segment. The remaining segments are dominated by fine sediment, largely sand (Figure 14). Segments 2 and 4 have over 8% fine substrate, while segments 1, 3, and 5 have a greater proportion of hard substrate, between 2 and 45% (Figure 15). We know this abundance of sand is due both to the geology and slope of the river and to historic logging and land use practices which contributed large amounts of sand. Although there is clearly an overabundance of fine sediment in segments 2 and 4 (Figure 15), there are also some sizeable areas of gravel in segments 3 and 5 (Figure 14). It is difficult to determine if the gravel present in these segments is sufficient for the coldwater fishery. The abundance of gravel and riffles present, is similar in scope to other northern Michigan trout streams surveyed, that are known for good reproduction and recruitment (e.g., Black River, Little Manistee River). Additional hard substrates and riffle habitats may increase the spawning and reproduction capacity of the river. An in-depth look at existing fisheries data from the different segments of this river may be needed to help verify limiting factors; or new surveys may be needed to help fill data gaps for some stream segments.

26 Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat Substrate Composition by Segment Segment 1 Segment 2 Segment 3 Segment 4 Segment 5 Boulder Cobble Gravel Sand Silt Clay Figure 14. Upper Manistee River substrate composition by segment Substrate Composition by Segement Segment 1 Segment 2 Segment 3 Segment 4 Segment 5 Hard Fine Figure 15. Upper Manistee River fine (clay, silt, and sand) and hard (gravel, cobble, and boulder) substrate composition by segment.

27 Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat 27 Portage Creek Analysis: By Segment The 3 habitat mapping sites in Portage Creek were organized into 2 distinct segments for in-depth habitat analysis. Segments were grouped based on distinct changes in river habitat to allow for analysis of similar sections of river. Segment 1 consists of sites 1-2. These sites were grouped because of their relatively high abundance of fine substrates. Segment 2 consists of site 3 and was separated because of the relatively high abundance of hard substrate and deep water compared to sites 1-2 (Table 4, Figures 16, 17, and 18). Bedform Structure In Portage Creek there is limited riffle and pool habitat; this is also true when the stream is looked at in smaller segments (Figure 16). Both segment 1 and 2 are mostly run habitat, with less than 5% pool habitat, and no measureable riffle habitat (Figure 16) Bedform Strucutre by Segment Segment 1 Segment 2 Pool Riffle Run Figure 16. Bedform structure of segments in Portage Creek. In-stream Habitat Availability Portage Creek has abundant in-stream fish habitat. All segments have over 8% cumulative fish habitat, which is very high (Figure 17, Figure 11-D). Segment 1 has greater than 9% fish habitat (Figure 17). In segment 1, there is large amount of aquatic vegetation and wood, while in segment 2 there is an abundance of deep water habitat (Figure 17). This may be in part due to the presence of an old sand trap in segment 2, regardless in-stream habitat does not seem to be a limiting factor for Portage Creek.

28 Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat In-stream Habitat by Segment Segment 1 Segment 2 Vegetation Wood Deep Figure 17. In-stream habitat structure in Portage Creek. Substrate Composition Sand is the most common substrate in both segments of Portage Creek. Hard substrate (gravel and cobble) does not dominate in any segment. The remaining segments are dominated by fine sediment, largely sand (Figure 18). Both segments have over 8% fine substrate (Figure 19). We know this abundance of sand is due to the geology and slope of the river, however land use practices may also be a contributing factor. Although there is clearly an overabundance of fine sediment in segments 1 and 2 (Figure 19), there are also some sizeable areas of gravel in segment 2 (Figure 18). It is difficult to determine if the gravel present in this segment is sufficient for reproduction in this tributary. Additional hard substrates and riffle habitats may increase the spawning and reproduction capacity of the stream. A fisheries survey of this stream may help verify and fine tune limiting factors.

29 Percent of River Percent of River Upper Manistee River Habitat A report on Upper Manistee River fisheries habitat Substrate Composition by Segment Segment 1 Segment 2 Boulder Cobble Gravel Sand Silt Clay Figure 18. Portage Creek substrate composition by segment. Substrate Composition by Segment Segment 1 Segment 2 Hard Fine Figure 9. Portage Creek fine (clay, silt, and sand) and hard (gravel, cobble, and boulder) substrate composition by segment. Recommendations and Management Actions Upper Manistee River Watershed Manistee River Segment 1 Segment 1, Mancelona to County Road 612 is dominated by run habitat, fine sediments, and has abundant fish cover. There is limited pool and riffle habitat present in the section. However, fisheries surveys seem to indicate that this segment of river does support spawning activity. Although this

30 3 segment has ample deep water, it does have less than most other segments of the Upper Manistee River, in addition it has relatively abundant wood and aquatic vegetation and therefore can be expected to support smaller size classes of trout. The combination of limited spawning habitat and great cover for juvenile fish seems to combine to allow for very high survival of young fish, leading to a high abundance of juveniles even with limited spawning habitat available. Actions to be considered: - Protection of key pool and riffle habitat from sedimentation. Ensure that sand from severe bank erosion sites, road stream crossings, and other sources is prevented from entering this section of stream; if sedimentation of pools is observed, consider wood installations that focus flows for scouring to ensure pools and deep water are maintained. Upper Manistee River Segment 2 Segment 2, County Road 612 to M-72, is dominated by run habitat, sandy sediment, and has the lowest percent of in-stream habitat of the Manistee River segments surveyed. Given this, this segment should be considered to be a key area for improvement. There is less fish cover in this segment than most (2% deep water, 16% wood, and 18% vegetation), although this is still high as compared to other systems studied. Work in segment 2 would be well-served to focus on increasing the complexity of substrate and bedform type in addition to fish habitat. If future work is pursued on the Upper Manistee, it would be advisable to focus efforts on segment 2. - Wood material augmentation would be undertaken to increase fish cover and provide additional areas for sediment storage. The entire reach may benefit from an overall increase in wood material for fish cover. - Ensure that sand from either upstream, severe bank erosion sites, roads, or other sources are prevented from delivering sand to this section of stream. - Add larger instream wood structures with designs that would promote localized bed scouring, adding cover but also unique deep water habitats and localized gravel substrates may result. Many possible designs exist for these purposes. The key elements would be stable installation with the objective of addressing the wide/shallow stream shape with localized areas that are narrower/deeper and sustainable (increased water velocities to prevent sand deposition in them). Upper Manistee River Segment 3 Segment 3, M-72 to Yellow Trees, has relatively diverse fish habitat with the highest amount of combined fish cover. It also have a relatively high portion of gravel substrate. It is however, completely dominated by run habitat. This segment appears to be relatively high quality habitat, to be monitored and protected from degradation. There is ample deep water (58%), wood (32%), and aquatic vegetation (15%). There is no documented pool or riffle habitat present in this segment, however there is enough deep water habitat present that the lack of categorized pool habitat is not concerning. An increase is

31 31 riffle habitat would be beneficial, however the lack of riffle in this segment may be largely due to the slope of the stream as there is still a reasonable amount of gravel present, even without any categorized riffle habitat. Activities in this segment should focus on preserving and protecting the habitat present. - Ensure that sand from either upstream, severe erosion sites, roads, or other sources are prevented from delivering sand to this area. - Establish long-term monitoring sites within this segment, where substrate conditions would be periodically monitored to detect any sedimentation that might occur. This could be done through monumented cross-sections at several riffles, where pebble count methods would be used, analyzed, and repeated annually or semi-annually. Upper Manistee River Segment 4 Segment 4, Yellow Trees to Lease 35, is dominated by run habitat (9%), with minimal riffle and pool habitat present. Segment 4 also has limited hard substrate (11%) and relatively low quantities of wood (16%) and aquatic vegetation (11%). There is an abundance of deep water habitat, which may contribute to the limited aquatic vegetation. The limited pool habitat present is tempered by the abundance of deep water. This segment would benefit from an increase in habitat complexity with a focus on increasing the amount of wood. The wood and vegetation in this deep water section is fairly limited, making much of the deep water habitat here likely less productive than it could or should be. - Increase instream wood material in this section to provide better fish cover. Wood material additions here would be primarily for the objective of fish cover, not necessarily for channel morphology changes. - Protection of key deep water habitat from sedimentation. Ensure that sand from severe bank erosion sites, road stream crossings, and other sources is prevented from entering this section of stream; if sedimentation of pools is observed, consider wood installations that focus flows for scouring to ensure pools and deep water are maintained. Upper Manistee Segment 5 Segment 5, Lease 35 to Sharon, has the highest quality habitat of the water surveyed in the Upper Manistee. This section is almost half gravel, it also has the lowest percentage of run habitat of the segments surveyed. There is still fairly limited pool (3%) and riffle (16%) habitat, however it is much more diverse than the other segments. There is also ample fish cover available, though an increase in wood and aquatic vegetation would be beneficial. However, given the diversity of this segment instream habitat work is not a high priority. - Establish long-term monitoring sites within this segment, where substrate conditions would be periodically monitored to detect any sedimentation that might occur. This could be done through monumented cross-sections at several riffles, where pebble count methods would be used, analyzed, and repeated annually or semi-annually.

32 32 - Ensure that sand from either upstream, severe bank erosion sites, roads, or other sources are prevented from delivering sand to this section of stream. - Protection of key riffle and pool habitat from sedimentation. Ensure that sand from severe bank erosion sites, road stream crossings, and other sources is prevented from entering this section of stream; if sedimentation of pools is observed, consider wood installations that focus flows for scouring to ensure pools and deep water are maintained. Portage Creek Segment 1 Segment 1, Euclid Avenue to Trout Trail, is dominated by run habitat and sand sediment. There is a very small amount of pool habitat present. This segment does have extensive fish cover in the form of wood and aquatic vegetation but does have a very limited amount of deep water. Given this, this segment should be considered to be a key area for improvement. Work in segment 1 would be well-served to focus on increasing the complexity substrate and bedform type in addition to deep water. If future work is pursued Portage Creek, it would be advisable to focus efforts on segment 1. - Use of brush bundles and smaller wood material placed on the shallow stream margins to foster deposition of fine sediments within them to promote narrower/deeper stream channels in select locations. The use of these brush bundles for sediment capture and stream narrowing could be downstream of larger installations done for the purpose of creating localized scour and pools (to capture the sediment scoured rather than sending it downstream into other portions of the Portage Creek). - Ensure that sand from either upstream, severe erosion sites, roads, or other sources are prevented from delivering sand to this area. - Establish long-term monitoring sites within this segment, where substrate conditions would be periodically monitored to detect any sedimentation that might occur. This could be done through monumented cross-sections at several riffles, where pebble count methods would be used, analyzed, and repeated annually or semi-annually. Portage Creek Segment 2 Segment 2, Trout Trail to Upper Manistee River, segment 2 is dominated by run habitat and sand sediment. However, there is more gravel and cobble substrate in segment 2 than segment 1. In addition, segment two has an abundance of wood and deep water habitat. There is limited aquatic vegetation, however that is likely in part due to the water depth in this section. Fisheries surveys in segment 2 may help better identify any limiting factors in this section. - Complete fisheries population estimates in segment 2 to identify issues with reproduction or recruitment. - Establish long-term monitoring sites within this segment, where substrate conditions would be periodically monitored to detect any sedimentation that might occur. This could be done

33 33 through monumented cross-sections at several riffles, where pebble count methods would be used, analyzed, and repeated annually or semi-annually. - Ensure that sand from either upstream, severe erosion sites, roads, or other sources are prevented from delivering sand to this area. Overall Prioritization Prioritizing protection and enhancement efforts is often a difficult process, which by necessity needs to explicitly consider: 1.) current status of the river and its fisheries, 2.) certainty of benefits to be derived by the activities, 3.) risk of creating unintended negative consequences, 4.) feasibility of the projects contemplated including coordination & management, funding, permitting and regulations, and access, 4.) the array of stakeholder values and motivations for undertaking such efforts. This habitat assessment report is intended to help contribute to elements 1, 2, and 3. Elements 4 and 5, along with the others, will be up to all those engaged in stewardship of the Upper Manistee River to consider. With that said, from the results of this instream fish habitat assessment, the following general priorities are offered as a starting place for further discussions that follow. Tier 1 Priorities - Increase fish cover (wood) within run bedforms in Upper Manistee segment 2. - Increase fish cover, and bedform diversity promoting structures in Upper Manistee segment 2. - Utilize wood structures to create narrower and deeper habitat in Portage Creek segment 1. - Institute long-term sedimentation monitoring strategies described for Upper Manistee segments 3 and 5. MITU would be glad to work with others to set this up and provide analysis of results. It would involve a dedicated volunteer to do the monitoring, or several riparian landowners able to monitor one site annually or semi-annually. Tier 2 Priorities - Consider conducting fishery population estimates at several locations throughout Portage Creek. Fishery population data will help relate what we see as opportunities for habitat improvement with current fishery conditions. MITU will be glad to help select sites and conduct sampling, if desired - Consider possible enhancement efforts mentioned for segment 4, targeted in specific locations. - Consider expanding the instream fish habitat assessment to any other significant tributaries of the Upper Manistee River. MITU will be glad to assist in identifying all the tributaries, and developing a practical and feasible strategy towards their assessment.