PREPARED FOR:
Nestucca / Neskowin Watershed Council

PREPARED BY:
Steve Trask
Bio-Surveys,LLC.
Po Box 65
Alsea, Or.
97324

FUNDED BY:
Oregon Watershed Enhancement Board

RAPID BIO-ASSESSMENT 2003

INTRODUCTION

             A Rapid Bio-Assessment inventory was conducted for the Nestucca / Neskowin Watershed Council (NNWC) during the summer of 2003. This inventory included the Nestucca, Neskowin and Sand Lake basins. The intent of the project was to gather information on the status of juvenile salmonid summer distributions and summer rearing densities. The inventory consists of extensive snorkel surveys in each basin that begin at the head of tidal influence and continue to the end of juvenile Coho distribution in each stream and its tributaries (mainstem Nestucca begins at the confluence of Beaver Cr.).  These surveys were conducted using funds granted to the NNWC by OWEB.  The intent of these surveys is to develop base line data for each of three successive cohorts and to eventually identify long term trends in the distribution and abundance of juvenile Coho, Steelhead, Cutthroat and Chinook at the 6^th field level in response to restoration and watershed management issues.

            The escapement of adult Coho in all of the surveyed basins and ocean tributaries during the 2001and 2002 brood years has remained insufficient to adequately seed the summer habitat currently available on a watershed scale throughout the four 5^th fields in the NNWC management area. For many of the basins and subbasins, adult escapement is the primary limiting factor for production. The trend in the adult escapement of Oregon Coast Natural (OCN) Coho since 1990 has been positive for all of the NNWC basins with the highest recorded escapement in the last 13 years occurring in 2002. The Nestucca OCN Coho estimate for 2001 based on randomly selected adult spawning surveys was 3,940 and the Neskowin / Sand Lake estimate was 71. This figure more than tripled for 2002 rising to 13,068 while summer parr abundance almost doubled. The Neskowin / Sand Lake combined estimate for 2002 was only 16. These estimates exhibit dramatic increases in abundance and are indicators of recent improvements in ocean conditions. ODFW’s long term SRS monitoring of adult Coho escapement suggests that the 13 year trend for the North Coast monitoring area is one of only two statistically significant trends observed in the five coastal monitoring areas. This statistically significant trend was also detected in the more intensive monitoring associated with the Oregon Plan conducted between 1997 and 2001 (E-Map). Both methods suggest that the trend is driven primarily by abundance in the Nehalem River but that a significant positive trend is also quantifiable in the Nestucca.

It is important to recognize the significant role that changes in adult escapement can have on the observed distributions and densities of juvenile salmonids.  The resultant distribution data from 2003 still does not describe all of the accessible and suitable spawning and rearing habitats for salmonids because of continued under escapement.

            The survey method was designed to look at a sub sample (20%) of rearing habitats using a Rapid Assay technique that could cover large distances and succeed in describing the current distribution of Coho and quantify the rearing densities of Coho and the relative abundance of Cutthroat, Steelhead and Chinook in all of the surveyed streams and their tributaries.

            The database contains the results of 194 stream miles that were surveyed. This includes the full extent of Coho distribution in the Sand Lake (5.5 miles), Neskowin (10.6 miles) and Nestucca basins (146 miles) except for the segment of the mainstem Nestucca between the head of tidal influence and the confluence of Beaver Cr. and the majority of West Beaver (inadequate visibility). If a stream is not included in the database it was not surveyed. This will occur only in situations where a mapped tributary was dry or where there was a lack of suitable visibility for the survey methodology.

METHODS

            The basins and sub-basins surveyed were selected and prioritized by ODFW, BLM, USFS and NNWC technical advisors.  Survey crews were concentrated within a basin to complete the sampling activity within a concise window of time.  This approach led to transportation efficiency and eliminated any possibility of population shifts in response to changes in flow or temperature. This strategy was altered for the mainstem Nestucca where local knowledge from the technical advisory panel of the NNWC indicated that visibility in the lower mainstem could degrade during the summer months because of temperature driven algal blooms. This resulted in a hiatus of 24 days between surveys on the mainstem Nestucca between the first 10.7 miles surveyed in June above the confluence of Beaver Cr. and the remaining 22.2 miles surveyed in July and August to the end of Coho distribution. This hiatus was a replicate of the methodology utilized in year 1 of the RBA inventory to retain consistency in the methodology.

            Land owner contacts were made for all of the private, industrial and public ownerships that existed on both sides of every stream reach surveyed.  Developing these contacts involved extensive research in the county tax assessor’s office and then a personal contact to describe the survey and request permission for access. The land owner information was recorded (name, contact #, tax lot # and location) and will be available in subsequent years as a byproduct of this contract.

            Most surveys were initiated by randomly selecting any one of the first five pools encountered.  The protocol however was altered for small tributaries (2^nd order) where Coho presence or absence was undetermined, in these tributaries, the first pool above the confluence was selected as unit number one. This alteration in protocol was adopted to identify minor upstream temperature dependant migrations that may not have extended more than a few hundred feet. The identification of this type of migratory pattern in juvenile salmonids is critical for understanding potential limiting factors within the basin (temperature, passage, etc.). Some surveys were initiated at a point above brackish water influence or above agricultural influence where visibility conditions shifted from poor to good. In these surveys the start point of the survey will be indicated separately on the USGS quads available through the NNWC.

            The survey continued sampling at a 20% frequency (every fifth pool) until at least two units without Coho were observed.  In addition, pools that were perceived by the surveyor as having good rearing potential (beaver ponds, complex pools, tributary junctions) were selected as supplemental sample units to insure that the best habitat was not excluded with the random 20 percent sample. This method suggests that the data existing in the database could tend to overestimate average rearing density if these non-random units were not removed prior to a data query (the selected units are flagged as non-random in the database).

In subbasins with low rearing densities, there were situations where Coho were not detected for more than two sampled units.  These situations were left to the surveyors discretion, whether to continue or terminate the survey. There is a possibility that very minor, isolated populations of juvenile Coho could be overlooked in head water reaches of small 2^nd order tributaries. This tributary would have to include a strong beaver population that would impound emergent fry and truncate their normal downstream fry distribution patterns.

            Pools had to meet minimum criteria of being at least as long as the average stream width. They also had to exhibit a scour element (this factor eliminates most glide habitats) and a hydraulic control at the downstream end. There were no minimum criteria established for depth.  Only main channel pools were sampled.  Side channel pools, back waters and alcoves were not incorporated into the surveyed pool habitats. The primary reasons for not including these secondary and off channel pools is that they are typically not highly productive summer rearing locations and they compromise the consistency of measuring, summarizing and reporting lineal stream distances.

            The lineal distances represented in the database were estimated by pacing from the beginning of one sampled unit to the beginning of the next sampled unit.  The length of the sampled pool is an independent quantity, which was always measured and not estimated.  A minimum of three lineal estimates were also measured with a hip chain for each surveyed stream to develop a calibration factor for each surveyors estimate of distance.  Total distances represented in the database are consistently greater than map wheeled distances using USGS 1:24,000 series maps. This is related to the level of sinuosity within the floodplain that is not incorporated in mapping. If you are attempting to overlay this database on existing stream layer information there would be a need to justify lineal distances with known tributary junctions (these can be found in the comments column). In addition, the USFS under contract to the NNWC will be producing a digitized stream layer of Coho distribution for incorporation into the current GIS database.

Pool widths were generally estimated.  Because pool widths vary significantly within a single unit, a visual estimate of the average width was considered adequate.  Pool widths were typically measured at intervals throughout the survey to calibrate the surveyor’s ability to judge distance.

            The snorkeler entered the pool from the downstream end and proceeded to the transition from pool to riffle at the head of the pool.  In pools with large numbers of juveniles of different species, multiple passes were completed to enumerate by species. (Coho first pass, 0+ trout second pass, etc. ). This allowed the surveyor to concentrate on a single species and is important to the collection of an accurate value. In addition, older age class Steelhead and Cutthroat were often easier to enumerate on the second pass because they were concentrating on locating food items stirred up during the surveyors first pass and appeared to have less of their initial avoidance behavior.

            In large order stream corridors (mainstem Nestucca), two snorkelers surveyed parallel to each other, splitting the difference to the center from each bank.

            A cover/complexity rating was attributed to each pool sampled. This rating was an attempt to qualify the habitat sampled within the reach. The 1 - 5 rating is based on the abundance of multiple cover components within a sampled unit (wood, large substrate, undercut bank, overhanging vegetation). Excessive depth (>3 ft) was not considered a significant cover component. The following criteria were utilized:

1          0 cover present

2          1-25   %   of the pool surface area is associated with cover

3          26-50 %   of the pool surface area is associated with cover

4          51-75 %   of the pool surface area is associated with cover

5          > 75   %   of the pool surface area is associated with cover

            A point to consider here is that the frequency of higher complexity pools increases with a decrease in stream order. This inverse relationship is primarily a function of average channel width and the resultant ability of narrow channels to retain higher densities of migratory wood. Channel morphology begins to play a much more significant role in this relationship during winter flow regimes where increases in floodplain interaction and the abundance of low velocity habitat may become as significant as wood complexity.

A numerical rating was given to each sampled unit for the surveyor’s estimate of visibility. The following criteria were utilized:

Visibility                                                                

1          excellent                                                    

2          moderate                                                   

3          poor                                                           

            This variable delivers a measure of confidence to the collected data. Survey segments with a measure of 1 can assume normal probabilities of detection (the observed is within 20 percent of the actual for Coho). Segments with a measure of 2 suggest that less confidence can be applied to the observed number (uncalibrated) and segments with a visibility rating of 3 suggest that the observation can probably be used for only an assessment of presence or absence.

            There was also commentary recorded within each of the surveyed reaches that included information on temperature, tributary junctions, culvert function, the abundance of other species and adjacent land use. This commentary is included in only the raw Access database under the “comments” field and not in the Excel cd.

            The database contains fields designed to facilitate the development of a GIS data layer. These are LLID location numbers that are unique for each stream segment and latitude and longitude coordinates collected for unique features. Lat / Long coordinates are reported in degrees, minutes and seconds. Latitude and longitude values were not collected for start points because these values already exist in the actual LLID number used to initiate a surveyed reach.

            Latitude and longitude values were collected with a “Garmin 2 plus” GPS receiver with an external antenna. Many end point determinations were not verified with GPS coordinates because of the lack of reception.

 GENERAL OBSERVATIONS

The distribution and abundance of Coho juveniles observed during the 2003 summer field season was the result of a wide spread increase in adult escapement during the 2002 brood year. Estimates of adult escapement for the 2002 brood in the Nestucca exhibited a large increase (232%) from the previous year (ODFW SRS estimate) which resulted in a 92% basin wide increase in the 2003 summer rearing population of Coho. In addition, distribution of summer Coho parr in the basin was expanded by approximately 12 miles from the previous year. Summer parr estimates for the Neskowin basin improved by 36 % and decreased by 29% in the Sand Lake basin. ODFW adult estimates for these two basins were combined and indicated a 78% decrease in adult abundance for the 2002 brood.

Most habitats are still not seeded to capacity in the inventoried systems and there remains extensive summer habitat available to salmonids that are currently under utilized. There were some exceptions, Baxter, Bear, East Beaver, Elk, Louie, Sourgrass, and Trib B of the Nestucca exhibited a fully seeded condition for Coho during both the 2002 and 2003 inventories. These tributaries represent important anchor habitats for OCN Coho. For the following review, we are considering 1.5 fish / sq.meter a fully seeded density for Coho. There are concerns from many biologists that this estimate of fully seeded does not represent the production potential that exists in completely functional Coho habitat that is benefiting from the nutrient loading of adult spawning salmonids (eggs, carcasses). There are excellent examples in Elk Cr., Baxter Cr., and East Beaver Cr. of stream reaches that far exceed the level of 1.5 fish/sq.meter of pool surface area. The intent of establishing this target of full seeding is to provide a platform for comparing stream reaches to each other and to themselves over time. The graphics available in the Nestucca / Neskowin cd utilize this value to normalize scaling.

            The average density for a surveyed reach is an excellent measure of trend that can be monitored from year to year. However, it tends to portray only a general description of the current status within a reach. Understanding how each reach is functioning is more accurately interpreted in a review of how the rearing density changes within the reach. The graphics provided in electronic format with this summary are essential for the proper interpretation of this review (refer to 2003 Nestucca / Neskowin cd, NNWC).

Distribution profiles

            The distribution of juveniles and their observed rearing densities for each surveyed reach provide a basis for understanding how each reach is functioning in relation to the remainder of the basin or subbasin. These profiles can help identify spawning locations, identify potential barriers to upstream adult and juvenile migration, identify the end point of Coho distribution and they may also indicate how juvenile salmonid populations are responding to environmental variables such as increased temperature. You will find a review of these distribution profiles within this document for each of the major basins and subbasins surveyed during the 2003 field season. Trend analysis will become an important aspect of this review upon completion of the 2004 inventory, concluding three continuous years of monitoring.

Location of spawning destinations

The approximate locations of spawning pairs was observable in many of the sampled sub basins by the presence of a distinct spike in rearing density that trailed off rapidly just upstream. The physical location of a spawning destination has a range of variance plus or minus 4 pools due to the 20 percent sample methodology.  Depending on the average distance between pools, this typically describes a maximum lineal distance that varies between 150 ft. in a small 2nd order tributary to 800 ft. in a fourth order tributary. To utilize the database to identify spawning destinations, an additional precaution is necessary. Surveyed lineal distances are typically longer than calculated distances (map wheel, GIS, etc.) due to the sinuosity of the active channel that is not displayed in the 1:24,000 series USGS maps. To accurately evaluate site specific locations it is important to utilize the digitized map layer that has been justified to known end points and tributary junctions. This layer is currently being developed by the USFS and is available from the Nestucca / Neskowin Watersheds Council.

            The average densities generated represent a snapshot in time of the current condition that can be compared to known levels of abundance that exist in fully seeded and fully functional Coho habitats. These densities also provide a method for quantifying changes in rearing densities by reach or subbasin over time. Average densities utilized as a metric in this analysis are calculated for pool surface areas only. Lower levels of Coho abundance exist in fast water (riffle/rapid) and glide habitats. Replicate surveys conducted in these same reaches in subsequent years will function as an indicator of response to future restoration and enhancement strategies and potential changes in land use. It does not however, provide any indication of actual smolt production because of the distinct relationship between juvenile Coho survival and the abundance of high quality winter habitat.

Adult and Juvenile Barriers

                Adult migration barriers are verified by determining that no juvenile production is occurring above a given obstruction (culvert, falls, debris jam, beaver dam, etc.). There are many barriers, both natural and manmade that impact the migration of salmonids in coastal basins. Some are definitive barriers that are obvious obstructions (such as the bedrock falls on the Little Nestucca below the confluence of Fall Cr.). Many barriers however, only impede adult salmonid migrations during low flow regimes. Summer juvenile inventories allow us to definitively quantify whether passage was obtained at any point during the season of adult migration.

            Juvenile salmonids typically migrate upstream for a variety of reasons (temperature, winter hydraulic refuge, food resources). Hydraulic refuge and food resources are typically fall, winter and spring migrations that would not be detectable during summer population inventories. Temperature however, is probably the most significant driver of upstream juvenile salmonid migrations during summer flow regimes. Juvenile barriers are subjective to the eye of the observer. The trend in juvenile density can be a method of detecting either partial or full barriers to upstream migration. Each of the surveyed reaches contains a comments section in the Access database to note the presence of culverts, jams and other physical factors that may influence the ability of salmonid populations to make full use of aquatic corridors.

 Temperature Dependant Migrations

 Potential temperature dependant migrations can be observed in the database by looking for densities that decrease significantly as the lineal distance increases from the mouth of the stream or tributary. This is more likely to be observed in the case of low abundance years where tributary habitats that are seeded to capacity are the exception. During years of high abundance there is a more significant potential for density dependant upstream migrations that would be indistinguishable from the distribution pattern mentioned above. The recognition of this migration pattern allows us, during years of low escapement, to identify important sources of high water quality within the basin that may be traditionally overlooked because of some other morphological condition that suggests to us that there is no significant potential for rearing salmonids (i.e. lack of spawning gravel). These stream reaches typically exhibit declining densities with increased distance from the mouth and no indication of a spawning peak (a point near the upper distribution of the population with significantly higher rearing densities). These tributaries may be functioning as important summer refugia for salmonid juveniles threatened by increasing temperatures in the mainstems.

Precautions

            The specific location of spawning sites does not infer that the highest quality spawning gravels were targeted by adult salmonids or that there is any relationship between the location of a redd and the quality of the rearing habitat that exists adjacent to these locations.

            The location and distribution of juvenile Coho represented in the database is not related to the quality of the rearing habitat that exists in the aquatic corridor adjacent to these sites.

            The average densities that can be generated as an end product for each stream reach are the result of a 20 percent sample. Consequently, they probably vary significantly around the true average density. There are many sources of potential variation, start point, number of units sampled within the reach, surveyor variability, etc. The range of variability for at least one of these variables (start point), was documented in the final review of the 1998 Rapid Bio-Assessment conducted by Bio-Surveys for the Midcoast Watershed Council. To facilitate the proper utilization of the data included in this inventory, the 1998 results are included in Table 1. The true average density of a stream reach was retrieved by querying the database from an ODFW survey on East Fk. Lobster where every pool was sampled. Comparisons could then be made between the true average density and a randomly selected 20 percent sub sample (every 5th pool). Only mainstem pools were utilized within the range of Coho distribution to match the protocol for the Rapid Bio-Assessment. Table 1 contains this comparison, exhibiting the variation in average density based on the selection of different starting points.

(Table 1)

SAMPLE FREQUENCY     AVG. COHO DENSITY               AVG. SH DENSITY    AVG. CUT DENSITY    AVG. 0+ DENSITY

100 %                             1.07                                     .03                             .04                        .13          50                                  1.10                                      .04                             .03                        .14

20 % Start Pool 1             0.87                                      .04                             .03                        .13

20 % Start Pool 3             1.01                                      .03                             .03                        .13

20 % Start Pool 5             1.13                                      .05                             .04                        .12

                When calculating the average density of juvenile Coho in a particular stream reach, it is important that only the data be utilized that falls within the distribution of Coho. Many stream reaches contain sample sites that extend well above the actual distribution of juvenile Coho. Including these data points significantly underestimates the average rearing density and provides a poor foundation for monitoring trends in subsequent years. There are also many streams surveyed that have a downstream point of Coho distribution that is well above the start of the survey reach. Two factors for each stream reach surveyed are key elements for trend analysis, the extent of the distribution and the average density within that distribution.

SITE SPECIFIC OBSERVATIONS 

Site specific observations within this document have been organized in a format that utilizes GIS definitions to describe basins and subbasins. The area within the NNWC management zone includes four 5^th fields. Each of these 5^th fields has been summarized separately. The expanded juvenile salmonid estimates are also broken down into 5^th field estimates (i.e., the mainstem Nestucca does not include the production from the Little Nestucca).

Nestucca

The Nestucca mainstem was not surveyed below the confluence of Beaver Cr. because of compromised visibility resulting from suspended solids and algae. There is significant juvenile salmonid rearing that occurs in these 14.5 river miles between Pacific City and the confluence of Beaver Cr. (6.6 of these river miles are classified as intertidal, from the boat ramp in Pacific City to the head of tide at the Cloverdale bridge). This potential production has not been accounted for in the 4^th or 5^th field production estimates below.

The following tables represent the contribution in salmonid production (by species) from each tributary to the Nestucca 4^th field Watershed.  Table 2 represents results from 2003 inventories and Table 3 represents production within just the Main Nestucca 5^th field (minus the Little Nestucca subbasin). These production estimates are based on an expansion of the 20% snorkel sample in pools only and therefore do not constitute an entire production estimate for the basin. These estimates  greatly under estimate the standing crop of 0+, Steelhead and Cutthroat because a large component of the basins standing crop is summer rearing in riffle / rapid and glide habitats that were not inventoried. In addition, there is also production for these three groups that extends upstream beyond the end point of Coho distribution where the surveys were terminated. This table however, can be utilized to establish a baseline for trend monitoring for subsequent survey years on the basin wide scale and by tributary. The table functions well to establish relative production potentials that can be utilized as a foundation for prioritizing restoration opportunities.

Basin wide Coho production rose 92% in 2003 in response to the surge in adult escapement. The top five subbasins changed little from the previous year except for Moon Cr. taking the place of Bear Cr./Nestucca as #5. Improvements were seen in almost every subbasin and many small tributaries which had no Coho populations in 2002 were found with small numbers of rearing juveniles. Highest rearing increases were found in Powder Cr. (798%), Moon Cr. (533%), Little Nestucca Mainstem (327%), Niagra Cr. (265%), Mainstem Nestucca (91%), Three Rivers (70%), Elk Cr. (58%), and Bear Cr./Nestucca (40%). The only decreases were observed in the Louie Cr. subbasin of the Little Nestucca. Habitat reaches seeded to capacity were found in Elk Cr., Bear Cr./Nestucca, East Beaver Cr., and Baxter Cr.

Overall Steelhead production within surveyed reaches dropped by 11% in 2003. Increases were observed in Bear Cr./Nestucca (53%) and the Little Nestucca subbasin (26%) while the largest reduction in abundance was recorded in Moon Cr. (-44%), Mainstem Nestucca (-26%), and East Beaver Cr. (-18%). The top five subbasins for Steelhead production remained the same though their order has been somewhat shuffled. A dramatic 44% decline was noticed in 0+trout abundance during this year’s survey, mostly within the Nestucca mainstem and its upper tributaries. Based on this data, continued declines in 1+Steelhead and Cutthroat are expected in 2004 inventories.

(Table 2) 2003 INVENTORY