Prepared for Humboldt County Gravel Operators. Prepared by Stillwater Sciences 850 G Street, Suite H Arcata, CA 95521

Transcription

1 2007 Fisheries Monitoring Program Report for Gravel Extraction Operations on the Mad, Lower Eel, South Fork Eel, Van Duzen, and Trinity Rivers, California Prepared for Humboldt County Gravel Operators Prepared by Stillwater Sciences 850 G Street, Suite H Arcata, CA August 2008

2 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report Stillwater Sciences Fisheries monitoring program report for gravel extraction operations on the Mad, Eel, South Fork Eel, Van Duzen, and Trinity rivers, California. Prepared by Stillwater Sciences, Arcata, California for Humboldt County Gravel Operators. 27 August 2008 Stillwater Sciences i

3 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report Table of Contents 1 INTRODUCTION METHODS RESULTS AND DISCUSSION Mad River Lower Eel River South Fork Eel River Van Duzen River Trinity River REFERENCES...14 List of Tables Table 2-1. Companies participating in the biological monitoring program... 3 Table 3-1. Lengths and percentages for Mad River pool:riffle:flatwater habitat units Mad River Hatchery to the lower end of the O Neill Bar Table 3-2. Mad River pool depths for Mad River Hatchery to the O Neill Bar... 5 Table 3-3. Mad River salmonid habitat areas for Mad River Hatchery to the O Neill Bar... 6 Table 3-4. Lower Eel River pool:riffle:flatwater lengths and percentages for mouth of the Van Duzen River to Fernbridge... 7 Table 3-5. Lower Eel River pool depths for mouth of the Van Duzen River to Fernbridge Table 3-6. Lower Eel River mapped habitat unit areas for mouth of the Van Duzen River to Fernbridge... 9 Table 3-7. South Forth Eel River pool:riffle:flatwater lengths and percentages for Table 3-8. South Fork Eel River pool depths for Table 3-9. South Fork Eel River mapped habitat unit areas for Table Van Duzen River pool:riffle:flatwater lengths and percentages Table Van Duzen River pool depths for Table Lower Van Duzen River mapped habitat unit areas for Table Trinity River pool:riffle:flatwater lengths and percentages for Table Trinity River mapped habitat unit areas for List of Appendices Appendix A. Delineated Aerial Photographs Mad River Appendix B. Delineated Aerial Photographs Lower Eel River Appendix C. Delineated Aerial Photographs South Fork Eel River Appendix D. Delineated Aerial Photographs Van Duzen River Appendix E. Delineated Aerial Photographs Trinity River 27 August 2008 Stillwater Sciences ii

4 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 1 INTRODUCTION AND BACKGROUND Many northern California rivers draining areas underlain by Franciscan formation geology contain low-gradient depositional reaches that contain vast stores of cobble, gravel, and sand. The lower reaches of several of these rivers are currently being utilized to provide gravel-based products, such as concrete and asphalt, for a variety of public and private construction projects. These operations provide a valuable commodity necessary for the construction and maintenance of communities and infrastructure. Commercial gravel removal operations have occurred on the depositional reaches of rivers and creeks in Humboldt County since at least the 1950s. Extraction generally occurs on gravel deposits that have been annually replenished during the winter runoff. Because fish utilize the waterways where gravel is extracted from exposed bar surfaces, there is a heightened concern about the potential impacts these operations may have on the fishery resources. This is especially true given the Endangered Species Act (ESA) threatened listings and critical habitat designations for coho salmon (Oncorhynchus kisutch), Chinook salmon (O. tshawytscha), and steelhead trout (O. mykiss). Since 1997, the commercial gravel operators in Humboldt County have conducted fisheries monitoring activities as a requirement of the U.S. Army Corps of Engineers (USACE) Letter of Permission (LOP), Humboldt County Interim Monitoring Program (IMP), and individual Clean Water Act Section 404 permits. The terms and conditions of the biological opinions (National Marine Fisheries Service [NMFS] 2004a, 2004b) that cover gravel-mining activities in Humboldt County require monitoring to track habitat conditions for listed salmonids. As described in the biological opinions (NMFS 2004a, 2004b), the current monitoring program was developed collaboratively between the involved agencies and gravel mining companies. NMFS met with local and state agencies and companies in December 2004 and January 2005 to begin the collaborative process. In March 2005, NMFS sent out a draft monitoring plan for review and comment, and in June 2005, NFMS met with agencies and applicants to discuss and incorporate the comments. The current monitoring program was finalized and implemented in September The intent of the habitat monitoring effort is two-fold. The first is to maintain continuity from past habitat mapping efforts and record the distribution and characteristics of habitat units that provide fish habitat value, such as pool, riffles, and flatwaters. The second objective of the monitoring is to identify and quantify specific life history habitat parameters over time. This requires the identification and delineation of specific instream habitat units critical for spawning, rearing, and holding adult and juvenile salmonids. This monitoring report details the results of the 2007 biological monitoring program for instream gravel extraction operations on the Mad, Eel, South Fork Eel, Van Duzen, and Trinity rivers in Humboldt County. 27 August 2008 Stillwater Sciences 1

5 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 2 METHODS The biological monitoring program included collection of habitat data that described the distribution and characteristics of three principal habitat types as described by the California Department of Fish and Game (Flosi et al. 1998): pools, flatwaters, and riffles, with the addition of an alcove habitat. This habitat-typing effort was applied at each site, and extended, at a minimum, one-half of a meander sequence above and below a given extraction site. Habitat types (pools, riffles, flatwaters, and alcoves) were delineated on the current 2007 aerial photograph for the site(s). The maximum depth of pools and riffle crests were also recorded on the aerial photographs or derived from longitudinal profile data collected and/or supervised by licensed land surveyors. A habitat-mapping component was also incorporated into the monitoring program that delineated more specific micro-habitat features based on relevant salmonid life history stages of concern for each reach. Specific micro-habitats included individual locations within the rivers that provided adult salmonid-holding habitat (AH), Age 2+ steelhead-rearing habitat (2+), spawning habitat (SP), juvenile coho-rearing habitat (COHO), and alcoves (AL). Identification of individual micro-habitat locations were based on general habitat suitability criteria for salmonids. The habitat suitability criteria were developed from a literature review (Barnhart 1986, Bjornn and Reiser 1991, and Reeves et al. 1989) with additional calibration by the fisheries biologist that included underwater and streambank observations of fish location, substrate characteristics, and spawning activity, as well as measurements of water depth and velocity. Preferred habitat for adult Chinook salmon consists of a pool with velocity of ft per second (fps) and depth greater than 3 ft. Age 2+ steelhead prefer to reside in run habitats where the water velocity is between 0.75 and 1.5 fps near the bottom, in depth of 1 3 ft, and have a cobble/small boulder substrate. Age 2+ steelhead also prefer head-of-pool habitats below the entry point of riffles. Spawning habitat typically occurs in a pool tailout or riffle where the water is ft deep, flowing at 1 3 fps, over a small gravel to small cobble substrate. Juvenile coho have been observed in the Mad River utilizing the margins of pool and flatwater habitat units with relatively slow ( fps) water velocities that contain overhanging and submerged vegetation. Alcoves are off-channel habitats located on the downstream end of gravel bars, and may provide velocity refuge for juvenile salmonids during high flows and potential thermal refuge during the summer season. The field habitat-mapping component was conducted concurrently with the habitat typing. The mapping required the biologist to identify the individual micro-habitats and delineate their perimeters on aerial photographs. With the exception of the Trinity River, where flows were too high, the biologist would periodically enter the water to conduct underwater observation, as well as measure depths and velocities to ensure accurate delineation of the habitat polygons. Each polygon was given an identification code based on salmonid life history stage use. Depth data were not collected on the Trinity River due to safety concerns. All habitat-mapping units were delineated based on the flow conditions present during data collection. No units were delineated based on the surveyor s projection of what conditions would look like if flows increased or decreased in the future. All habitat types and polygons were digitized into a Geographic Information System (GIS) program. The area (square feet) of the individual habitat polygons and lengths of individual 27 August 2008 Stillwater Sciences 2

6 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report habitat types were determined through the GIS and entered into a Microsoft Excel spreadsheet from which a series of tables was generated for this report. Data analysis included: determining the pool:riffle:flatwater percentages by length of the stream reach; determining residual pool depths; determining the area of the individual habitat polygons; comparing the habitat types and mapped habitat unit areas between years in the Mad River for the years 2002 (Halligan 2003), 2004 (Halligan 2005), (Halligan 2007), and 2007; and comparing the mapped habitat unit areas between years in the lower Eel, South Fork Eel, Van Duzen, and Trinity rivers for (Halligan 2007) and Biological monitoring was conducted in 2007 for the following aggregate extraction companies (Table 2-1): Table 2-1. Companies participating in the biological monitoring program. River Company Gravel Bar Mad River Sand and Gravel (MRS&G) Granite Construction Guynup Emmerson (E) Blue Lake (BL) Mad Johnson (J) Christie Eureka Ready Mix (ERM) Johnson - Spini (J-S) O'Neill Mercer-Fraser (M-F) Essex Eureka Ready Mix Hauck Lower Eel Mercer-Fraser Sandy Prairie Shamrock Materials Drake County of Humboldt Worswick Mercer-Fraser Cooks Valley South Fork Eel Randall Sand and Gravel (RSG) Randall Wallan and Johnson (W&J) Wallan Van Duzen Tom Bess Bess Leland Rock Rock Trinity Mercer-Fraser Willow Creek McKnight 27 August 2008 Stillwater Sciences 3

7 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 3 RESULTS AND DISCUSSION 3.1 Mad River The 2007 Mad River survey reach totaled 38,839 ft in length, which included the mainstem and secondary channels. The combined pool:riffle:flatwater percentages for the Mad River Sand and Gravel (MRS&G), Granite Construction, Eureka Ready Mix (ERM), and Mercer-Fraser (M-F) reaches were 22:19:60 (Table 3-1). The percentage of the survey reach consisting of pool habitat appeared to decrease between 2006 and 2007 (Table 3-1). However, the 2007 pool length percentage was 69% greater than in 2005 even though the survey s reach length increased by 32%, primarily due to the inclusion of secondary channel habitat data. The amount of riffle habitat was relatively consistent from 2005 through Flatwater percentages appeared to be inversely related to pool percentages (Table 3-1). Table 3-1. Lengths and percentages for Mad River pool:riffle:flatwater habitat units Mad River Hatchery to the lower end of the O Neill Bar. Operator/Bar Pools (ft) Riffles (ft) Flatwaters (ft) MRS&G/Guynup 840 2, ,026 1,804 3,207 2,292 2,802 Granite/E&BL 640 2,970 1,797 2,148 2,253 2,227 6,516 5,758 8,480 ERM/Christie 516 1,984 1, ,173 1,517 4,056 4,030 2,506 Granite/Johnson 624 1, ,628 1,720 2,745 M-F/Essex 687 1,140 1, ,944 1,928 ERM/J-S/O'Neill 575 1,030 2, , ,260 6,297 4,699 Total 3,882 10,537 8,530 5,095 7,316 7,151 20,417 22,041 23,158 P:R:F % Note: There was no requirement to collect pool:riffle:flatwater length data in The increase in survey reach lengths between 2005 (29,394 ft), 2006 (39,894 ft), and 2007 (38,839 ft) were due in large part to the collection of secondary channel habitat data. The 2007 residual depths throughout the survey reach ranged from 1.6 to 9.8 ft and were on average about 0.7 ft shallower than in (Table 3-2). In general, the number of pools within the survey reach increased significantly between 2005 and 2007, which may be due, in part, to the expansion of the survey reach or lack of data in The 2007 adult-holding, spawning, coho, Age 2+ steelhead, and alcove habitat areas within the extraction reaches covered 242,708 ft², 249,256 ft², 72,987 ft², 165,000 ft², and 118,178 ft², respectively (Table 3-3) (See Appendix A for delineated aerial photographs). Between 2004 and 2007, there appeared to be an increase in adult-holding, Age 2+ steelhead, and coho habitat areas (Table 3-3). This increase in habitat may have been due in part to the expansion of the survey reach. Spawning habitat quantity appeared to show a decrease in area. Alcove habitat area showed annual variation. There is an unknown amount of measurement error associated with the habitat-mapping effort. Measurement error could have been introduced into the data from several sources. First, the 2002 data should not be weighed as heavily as the data because the protocol was under 27 August 2008 Stillwater Sciences 4

8 Operator/Bar MRS&G/ Guynup Granite/ Emmerson Granite/ Blue Lake ERM / Christie Granite/ Johnson M-F/ Essex ERM J-S ERM/ O Neill 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report development and the flaws had yet to be resolved. Another source of errors may be caused by the different discharges between the dates when mapping was being conducted and the aerial photographs were flown. For example, discharges for the 2002, 2004, 2005, 2006, and 2007 habitat mapping efforts were cfs, cfs, cfs, cfs, and 352 cfs, respectively. The spring aerial photographs were taken when the river was at a higher discharge ( cfs). This resulted in estimating edges of habitat polygons in relation to morphological features that were submerged on the aerial photographs. Table 3-2. Mad River pool depths for Mad River Hatchery to the O Neill Bar. Maximum Depth (ft) Riffle Crest Depth (ft) Residual Depth (ft) nd <5 ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns ns Average Depth Notes: ns indicates no survey occurred. - indicates pools were not present even though the entire reach was surveyed. nd indicates no data collected. Depth data for MRS&G (2007), Granite (2005), ERM ( ) taken from longitudinal profiles. Pools do not necessarily occur in the same number or place every year. Therefore, the data can only be used for general comparative purposes and not to compare the depth of an individual pool through the years. 27 August 2008 Stillwater Sciences 5

9 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report Table 3-3. Mad River salmonid habitat areas for Mad River Hatchery to the O Neill Bar. Operator/Bar Adult Holding (ft²) Spawning (ft²) MRS&G/Guynup 16,100 44,867 47,916 74,488 44,403 44, ,722 58,806 58,370 62,102 Granite/E&BL 23,825 57,499 40,511 68,825 28,815 35, , ,434 85,813 32,161 ERM/Christie 24,900 54,450 44,867 31,364 47,338 47, ,938 65,340 68, ,440 Granite/Johnson 14,800 13,504 11,326 19,602 18,024 28,400 26,136 27,878 22,651 19,618 M-F/Essex 26,800 ns 14,375 32,670 20,199 28,600 ns 13,068 10,454 9,167 ERM/ J-S/O'Neill 25,650 43,560 33,106 14,375 83,930 23,000 23,522 21,780 20,038 2,768 Total 132, , , , , , , , , ,256 Operator/Bar Coho (ft²) 2+ Steelhead (ft²) MRS&G/Guynup 0 8,712 5,227 2,316 8,047 3,000 nd 21,780 23,087 39,670 Granite/E&BL 0 5,663 7,406 5,663 6,149 8,500 54,886 48,351 47,916 42,152 ERM/Christie 0 14,375 4,792 3,049 7,939 18,900 28,750 36,591 60,984 29,647 Granite/Johnson 9,325 17,860 19,062 17,860 7,654 4,450 43,560 23,522 9,148 12,099 M-F/Essex 2,800 ns ,900 ns 3,920 14,810 17,777 ERM/ J-S/O'Neill ,503 16,553 43,198 9, ,583 27,443 23,655 Total 12,125 46,610 49,990 45,441 72,987 52, , , , ,000 Operator/Bar Alcove (ft²) MRS&G/Guynup 0 5, ,534 16,391 Granite/E&BL 0 23,087 11,761 35,719 42,369 ERM/Christie 0 61,855 23,958 56,192 0 Granite/Johnson 13,800 19,166 27,443 25,265 21,110 M-F/Essex 0 ns 11,761 5,663 9,328 ERM/ J-S/O'Neill 34,500 5,563 15,246 4,972 28,980 Total 54, ,334 90, , ,178 Note: ns indicates no survey occurred. The 2002 data were collected as a pilot project to develop the habitat-mapping protocol, and as such, those data should not be viewed with as high a degree of confidence as August 2008 Stillwater Sciences 6

10 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 3.2 Lower Eel River The 2007 lower Eel River survey reach totaled 29,071 ft in length, which included the mainstem and secondary channels. The combined pool:riffle:flatwater percentages for the Eureka Ready Mix (ERM), Mercer-Fraser (M-F), Drake, and Worswick reaches were 16:8:76 (Table 3-4). The percentage of the survey reach consisting of pool habitat appeared to decrease between 2006 and 2007 (Table 3-4). However, the 2007 pool lengths were roughly the same as in The amount of riffle habitat was relatively consistent from 2005 to Flatwater percentages appeared to be inversely related to pool percentages (Table 3-4). Table 3-4. Lower Eel River pool:riffle:flatwater lengths and percentages for mouth of the Van Duzen River to Fernbridge. Operator/Bar Pools (ft) Riffles (ft) Flatwaters (ft) ERM/Hauck 1,180 2, ,008 1,013 1,595 1,365 4,098 M-F/Sandy Prairie 2,195 4,877 4, ,045 1,246 6,380 5,994 6,772 Shamrock/Drake 840 2, ,330 1,375 4,157 Humboldt Co./Worswick ,255 5,565 7,126 Total 4,215 9,494 4,659 1,390 2,438 2,259 19,560 14,299 22,153 P:R:F % Note: There was no requirement to collect pool:riffle:flatwater length data in The 2007 residual depths throughout the survey reach ranged from 4.3 to 11.4 ft and were on average about 0.6 ft shallower than in 2006 (Table 3-5). However, 2007 residual pool depths were deeper than those in 2004 and The number of pools within the survey reach decreased from eight in 2004 to four in Some of this pool loss may be attributed to sediment deposition and channel migration. For example, the loss of the Drake pool could be the result of deposition of bedload carried by the large secondary channel that is present on the west side of Sandy Prairie Island. In addition, one of the Sandy Prairie pools became an alcove when the upstream bar developed, which pushed the thalweg to the west. The 2007 adult-holding, spawning, Age 2+ steelhead, and alcove habitat areas within the extraction reaches covered 473,351 ft², 0 ft², 81,903 ft², and 91,417 ft², respectively (Table 3-6) (See Appendix B for delineated aerial photographs). Between 2005 and 2007, there appeared to be a decrease in adult-holding habitat. The decrease in adult-holding habitat could be attributed to the loss of pools in the Sandy Prairie and Drake reaches. In addition, even though the new Drake flatwater was greater than 3 ft deep, the low-water velocity (<0.5 fps) precluded it from being called adult-holding habitat. The lack of spawning habitat indicated that the lower Eel River is not used by salmonids for spawning. Even if spawning were to occur, the large amount of high flow bedload movement through the reach would result very low to non-existent redd survival. The Age 2+ steelhead habitat area was fairly consistent with what was recorded in 2006 and much greater than what was present in Alcove habitat area showed relative consistency between 2005 and 2006, but was reduced during The loss of alcove habitat area during 2007 was caused by the downstream growth of the Worswick Bar, which pushed the alcove entrance below Fernbridge and outside of the survey reach. No juvenile coho habitat was observed. 27 August 2008 Stillwater Sciences 7

11 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report There may be errors associated with the habitat mapping effort caused by the different discharges between the dates when aerial photographs were flown and when the mapping was conducted. For example, the 2005, 2006, and 2007 aerial photographs were taken when the river discharges at Scotia were 1,640, 1,090, and 1,870 cfs, respectively. Discharges for the 2005, 2006, and 2007 mapping efforts were 204 cfs, 113 cfs, and 74 cfs, respectively. This resulted in estimating edges of habitat polygons in relation to morphological features that were submerged on the aerial photographs. 27 August 2008 Stillwater Sciences 8

12 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report Table 3-5. Lower Eel River pool depths for mouth of the Van Duzen River to Fernbridge. Operator/Bar ERM/Hauck Maximum Depth (ft) Riffle Crest Depth (ft) Residual Pool Depth (ft) M-F/Sandy Prairie Shamrock/Drake Humboldt Co./Worswick Average Depth Notes: - indicates pools were not present even though the entire reach was surveyed. Pools do not necessarily occur in the same number or place every year. Therefore, the data can only be used for general comparative purposes and not to compare the depth of an individual pool through the years. Table 3-6. Lower Eel River mapped habitat unit areas for mouth of the Van Duzen River to Fernbridge. Operator/Bar Adult Holding (ft²) Spawning (ft²) 2+ Steelhead (ft²) Alcove (ft²) ERM/Hauck 65, ,971 39,521 8, ,206 21,787 29, ,107 13,883 M-F/Sandy Prairie 331,762 1,076, , ,448 52,854 44,578 23,292 77,534 Shamrock/Drake 100, , , Humboldt Co./Worswick 15, , ,787 0 Total 512,068 1,580, ,351 8, ,206 94,235 81, , ,186 91, August 2008 Stillwater Sciences 9

13 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 3.3 South Fork Eel River The 2007 South Fork Eel River survey covered three relatively isolated operations within the Cooks Valley to Redway reach and totaled 18,116 ft in length. The combined pool:riffle:flatwater percentages for the Mercer-Fraser (M-F), Randall Sand and Gravel (RSG), and Wallan and Johnson (W&J) reaches were 22:20:58 (Table 3-7). The pool:riffle:flatwater percentages remained fairly consistent between 2005 and 2007 (Table 3-7); this may have been due in large part to the bedrock-controlled nature of the river channel. Table 3-7. South Forth Eel River pool:riffle:flatwater lengths and percentages for Operator/Bar Pools (ft) Riffles (ft) Flatwaters (ft) M-F/Cooks Valley 1,530 1,717 2,035 1,330 1,158 1,304 3,685 3,567 3,894 Randall/Randall 1, ,028 1,168 1,377 1,550 4,223 4,644 3,815 W&J/Wallan 1, ,150 2,921 2,719 Total 3,880 3,463 4,062 3,253 3,012 3,626 10,058 11,132 10,428 P:R:F % The 2007 residual depths throughout the survey reach ranged from 2.1 to 20.2 ft and were on average about 1.6 ft shallower than in 2006 (Table 3-8). However, 2007 residual pool depths were about a half-foot deeper than those in 2004 and The observed loss of average pool depth between 2006 and 2007 is consistent with what was recorded on the Mad and Lower Eel rivers. The number of pools within the survey reach increased from 12 in 2005 to 16 in The 2007 adult-holding, spawning, Age 2+ steelhead, and alcove habitat areas within the extraction reaches covered 71,420 ft², 45,227 ft², 19,031 ft², and 0, respectively (Table 3-9) (See Appendix C for delineated aerial photographs). Between 2006 and 2007, there appeared to be a decrease in adult-holding habitat, which may be related to the reduction in pool depth. The reduction in the quantity of spawning habitat appeared to be due to coarsening of substrate in pooltails and riffle crests. The reduction in alcove habitat occurred at the Cooks Valley bar, where the usual alcove contained flowing water originating from a tributary and seepage through the gravel bar. This habitat unit also contained temperature-stratified water at the mouth of the tributary. There may be errors associated with the habitat mapping effort caused by the different discharges between the dates when aerial photographs were flown and when the mapping was conducted. For example, the 2005, 2006, and 2007 aerial photographs were taken when the river discharges at Miranda were 122, 207, and 240 cfs, respectively. Discharges for the 2005, 2006, and 2007 mapping efforts were 54 cfs, 29 cfs, and 22 cfs, respectively. This resulted in estimating edges of habitat polygons in relation to morphological features that were submerged on the aerial photographs. 27 August 2008 Stillwater Sciences 10

14 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report Table 3-8. South Fork Eel River pool depths for Operator/Bar Max Depth (ft) Crest Depth (ft) Residual Depth (ft) ns ns ns ns ns ns ns ns ns M-F/Cooks Valley ns ns ns ns ns ns ns ns ns ns ns ns Randall/Randall W&J/Wallan Average Depth Note: ns indicates no survey occurred. - indicates pools were not present even though the entire reach was surveyed. Pools do not necessarily occur in the same number or place every year. Therefore, the data can only be used for general comparative purposes and not to compare the depth of an individual pool through the years. Table 3-9. South Fork Eel River mapped habitat unit areas for Operator/Bar Adult Holding (ft²) Spawning (ft²) 2+ Steelhead (ft²) Alcove (ft²) M-F/Cooks Valley 56,153 55,784 56,747 22,056 54,178 14,187 nd 6,724 5,413 23,322 20,671 0 Randall/Randall 20,982 31,140 8,619 14,880 67,320 18,242 nd 5,301 8,845 2, W&J/Wallan 11,602 16,646 6,053 16,595 13,478 12,799 nd 7,603 4, Total 88, ,570 71,420 53, ,976 45,227 nd 19,628 19,031 26,205 20,671 0 Note: nd indicates no data collected. 27 August 2008 Stillwater Sciences 11

15 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 3.4 Van Duzen River The 2007 Van Duzen River survey reach totaled 11,442 ft in length and covered the Tom Bess (Carlotta) and Leland Rock (Alton) operations. The combined pool:riffle:flatwater percentages for the two reaches were 18:11:71 (Table 3-10). The pool:riffle:flatwater percentages remained fairly consistent between 2005 and 2006, but the proportion of the survey length made up of pools decreased from 2006 to 2007 (Table 3-10). The decrease in the 2007 pool percentage may have been due to (1) observed sediment intrusion into pools at Tom Bess operation, (2) lack of Noble pool data that typically accounts for about half the pool length in the gravel mining reaches, and (3) channel avulsion at the upstream end of the Leland Rock operation. Table Van Duzen River pool:riffle:flatwater lengths and percentages Operator/Bar Pools (ft) Riffles (ft) Flatwaters (ft) Tom Bess/Bess 1,281 1,296 1, ,449 4,860 4,632 Noble/Noble 2,176 2,567 ns 988 1,426 ns 5,589 4,729 ns Leland Rock/Rock 1,595 1, , ,281 2,471 3,317 Total 5,052 5,212 2,293 3,297 2,949 1,200 11,319 12,060 7,949 P:R:F % Note: ns indicates no survey occurred. Differences in total length between 2006 and 2007 were due mainly to a lack of Noble data (~8,700 ft). The 2007 residual depths throughout the survey reach ranged from 3.5 to 10.0 ft and were on average about 0.7 ft shallower than in 2006 (Table 3-11). The Van Duzen River extraction reaches appear to have experienced a significant decrease in pool depth since Much of the loss in the average residual pool depth stems from the deposition of sediment into the two deepest pools on the Bess property. The number of pools within the Bess and Rock reaches stayed fairly consistent between 2005 and The 2007 adult-holding, spawning, Age 2+ steelhead, and alcove habitat areas within the extraction reaches covered 33,505 ft², 1,817 ft², 11,540 ft², and 5,134 ft², respectively (Table 3-12) (See Appendix D for delineated 2007 aerial photographs). Between 2006 and 2007, there were significant decreases in adult-holding, Age 2+ steelhead, and alcove habitats. The reduction in the quantity of adult-holding areas appeared to be due to sediment deposition into pools, which resulted in shallowing and shortening of these habitat types. In addition, because no monitoring was conducted at the Noble site, significant amounts of adult-holding habitat data were not collected. Similarly, the perceived loss of Age 2+ steelhead habitat may have been due to a lack of Noble monitoring data. The bulk of the alcove loss was caused by the filling in of a single unit on Leland Rock s operation and lack of Noble data collection. There may be errors associated with the habitat mapping effort caused by the different discharges between the dates when aerial photographs were flown and when the mapping was conducted. For example, the 2006 and 2007 aerial photographs were taken when the river discharges at Bridgeville were 570 and 218 cfs, respectively. Discharges for the 2006 and 2007 mapping efforts were 8 cfs, and 7 cfs, respectively. This resulted in estimating edges of habitat polygons in relation to morphological features that were submerged on the aerial photographs. 27 August 2008 Stillwater Sciences 12

16 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report Table Van Duzen River pool depths for Operator/Bar Maximum Depth (ft) Riffle Crest Depth (ft) Residual Pool Depth (ft) Ton Bess/Bess Noble/Noble Leland Rock/Rock Average Depth Note: - indicates pools were not present even though the entire reach was surveyed. Pools do not necessarily occur in the same number or place every year. Therefore, the data can only be used for general comparative purposes and not to compare the depth of an individual pool through the years. Table Lower Van Duzen River mapped habitat unit areas for Operator/Bar Adult Holding (ft²) Spawning (ft²) 2+ Steelhead (ft²) Alcoves (ft²) Tom Bess/Bess 35,062 24, ,817 6,036 5,115 10,749 5,134 Noble 103,228 nd 0 nd 4,961 nd 27,562 nd Leland Rock/Rock 34,507 9, ,691 6,425 46,305 0 Total 172,797 33, ,817 16,688 11,540 84,616 5,134 Note: ns indicates no survey occurred. 27 August 2008 Stillwater Sciences 13

17 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 3.5 Trinity River The 2007 Trinity River survey reach totaled 9,290 ft in length and covered Mercer-Fraser s Willow Creek and McKnight bars. The combined pool:riffle:flatwater percentages for the two reaches were 55:26:19 (Table 3-13). The pool:riffle:flatwater percentages remained fairly consistent between 2006 and 2007, but the proportion of the survey length made up of pools increased from 2005 to 2006 (Table 3-13). The increase in pool habitat was mirrored by a decrease in flatwaters, while riffles remained stable. Table Trinity River pool:riffle:flatwater lengths and percentages for Operator/Bar Pools (ft) Riffles (ft) Flatwaters (ft) M-F/Willow Creek 1,564 2,618 2, , ,732 M-F/McKnight 1,605 3,324 2,723 2,101 1, ,222 2,114 0 Total 3,169 5,942 5,102 2,756 2,665 2,456 3,662 2,184 1,732 P:R:F % The 2007 adult-holding, spawning, Age 2+ steelhead, and alcove habitat areas within the extraction reaches covered 240,713 ft², 20,673 ft², 80,280 ft², and 0 ft², respectively (Table 3-14) (See Appendix E for delineated 2007 aerial photographs). Between 2005 and 2006, the amount of adult-holding habitat increased by about 40%. Between 2006 and 2007, the amount of holding habitat dropped by about 17%. The amount of spawning habitat in 2007 was about two-and-onehalf times than in 2005, but less than half of what was observed in The main reason for the reduction in spawning habitat between 2006 and 2007 appeared to be substrate coarsening. No Age 2+ steelhead habitat data were collected for the McKnight Bar in 2007 due to surveyor error. No alcove-like features were observed connected to the channel; however, the old trench at Willow Creek, which serves as an alcove, was present. The trench was not mapped as an alcove because it was not a naturally-formed feature. The secondary channel at the McKnight Bar would function as an alcove at higher flows. No pool depths were collected in the Trinity River due to unsafe flow conditions during data collection. Table Trinity River mapped habitat unit areas for Operator/Bar Adult Holding (ft²) Spawning (ft²) 2+ Steelhead (ft²) Alcove (ft²) M-F / Willow Creek 97, ,568 94,776 nd 18,547 14,225 nd 111,629 80,280 15,163 76,608 0 M-F / McKnight 108, , ,937 7,941 26,559 6,448 nd 25,326 nd 2, Total 205, , ,713 7,941 45,106 20, ,955 80,280 17,432 76,608 0 Note: nd indicates no data collected. There may be errors associated with the habitat mapping effort caused by the different discharges between the dates when aerial photographs were flown and the when mapping was conducted. 27 August 2008 Stillwater Sciences 14

18 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report For example, the 2005, 2006, and 2007 aerial photographs were taken when the river discharges at Hoopa were 1,350, 8,570, and 4,830 cfs, respectively. Discharges for the 2005, 2006, and 2007 mapping efforts were 713 cfs, 676 cfs, and 671 cfs, respectively. This resulted in estimating edges of habitat polygons in relation to morphological features that were submerged on the aerial photographs. 27 August 2008 Stillwater Sciences 15

19 2007 Humboldt County Gravel Extraction Fisheries Monitoring Report 4 REFERENCES Barnhart, R. A Species Profiles: Life histories and environmental requirements of coastal fishes and invertebrates (Pacific Southwest) Steelhead. Biological Report 82 (11.60). Prepared by California Cooperative Fishery Research Unit, Humboldt State University, Arcata, California for U.S. Army Corps of Engineers, Coastal Ecology Group, Vicksburg, Mississippi and U.S. Fish and Wildlife Service, National Wetlands Research Center, Washington, D.C. Bjornn, T. C. and D. W. Reiser Habitat requirements of salmonids in streams. American Fisheries Society Special Publication 19: Flosi, G., Downie, S., Hopelain, J., Bird, M., Coey, R., and Collins, B California salmonid stream habitat restoration manual. Third Edition. Inland Fisheries Division, California Department of Fish and Game. Halligan, D. H Final report fisheries monitoring program for gravel extraction operations on the Mad, Eel, Van Duzen, and Trinity Rivers. Natural Resources Management Corporation, Eureka, California. Halligan, D. H Unpublished Mad River instream habitat data. Natural Resources Management Corporation, Eureka, California. Halligan, D. H Final report fisheries monitoring program for gravel extraction operations on the Mad, Eel, Van Duzen, and Trinity Rivers. Natural Resources Management Corporation, Eureka, California. National Marine Fisheries Service (NMFS). 2004a. Batched biological opinion Mad River individual permits Eureka Ready Mix Concrete Company, Inc., Mad River Sand and Gravel, and Granite Construction. Prepared for the U.S. Army Corps of Engineers, San Francisco District. NMFS. 2004b. Biological opinion letter of permission procedure for gravel mining and excavation activities within Humboldt County. Prepared for the U.S. Army Corps of Engineers, San Francisco District. Reeves, G. H., F. H. Everest, and T. E. Nickelson Identification of physical habitats limiting the production of coho salmon in western Oregon and Washington. USDA Forest Service, Pacific Northwest Research Station. General technical report PNW-GTR August 2008 Stillwater Sciences 16

20 Appendix A Delineated Aerial Photographs Mad River

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31 Appendix B Delineated Aerial Photographs Lower Eel River

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37 Appendix C Delineated Aerial Photographs South Fork Eel River

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41 Appendix D Delineated Aerial Photographs Van Duzen River

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45 Appendix E Delineated Aerial Photographs Trinity River

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