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Cramer Fish Sciences: Lower American River   Innovative Scientific Solutions for Fisheries and Environmental Challenges  
Cramer Fish Sciences
"The U.S. Army Corps of Engineers funds hatchery programs in the Willamette Basin to help mitigate impacts from the development and operation of the system of multi-purpose dams. Cramer Fish Sciences assembled a database of historic information on stocking of hatchery fish in the Willamette Basin. Using this database, they provided an assessment of impacts to ESA-listed salmonids resulting from stocking of catchable rainbow trout. We were very pleased with the thoroughness and quality of their work products and we hope to gain their assistance with future projects."
Charles F. Willis
Fish Biologist
Portland District, USACE

PROJECT: Lower American River




Virtually all large California rivers are regulated by dams that provide power, water and flood protection to the world's eighth largest economy. This has created conflict between economic needs and protection of key ecological processes. In 2014, one of the most severe droughts in recorded California history pushed this issue to the forefront of scientific and political discussion. Reservoir storage in the American River, a key California water artery, was at an all-time low. In response, water released from the Nimbus Dam into the Lower American River (LAR) was reduced from ~1100 cfs to 500 cfs in four steps between 6-10 January 2014. This period coincided with fall-run Chinook salmon incubation, when much of the 2013/14 cohort was still within river gravels. This cohort represented the largest Chinook run in the American River system in the past eight years. Cramer Fish Sciences teamed up with local, state, and federal agencies to (1) determine the acute effects of this flow reduction on Chinook salmon, (2) develop a science-based process to make subsequent flow management decisions, and (3) monitor the effects of these decisions on incubating embryos and emerging and rearing fry.

Click images to see a full-size view.

Figure 1. Discharge

Figure 1. Hydrograph indicating flow (cfs) during the sample period. Red symbols indicate sampling events and arrows indicate fry emergence completion of 75, 95, and 99%, respectively.

Figure 2. Study Extent

Figure 2. Study Extent; Lower American River (LAR) showing the three study reaches and locations of sampling and areas that received gravel augmentation between 2008-2013.

Figure 3. Salmon impacts

Figure 3. Salmon impacts; Illustration highlighting impacts to different salmon life stages caused by dewatering and stranding following flow reduction on the LAR.

Figure 4. Redds Water's Edge

Figure 4. Redds Water's Edge; Dewatered areas at the Sailor Bar 2008 augmentation site, following flow reductions from 1100 to 500 cfs. On-the-ground redd survey data from 21-22 November 2013 is overlaid to show areas where redds were dewatered.

Figure 5. Salmon survival estimates

Figure 5. Salmon survival estimates

River flow reduction can cause salmon redds (nests) to be dewatered or stranded. Stranded embryos may become trapped and unable to emerge from the gravel or gain access to the main channel to complete development, rearing, and emigration. Reduced flow may have a more extreme impact on salmon embryos when weather is unusually warm or dry. This is because relatively warm air temperatures and lack of runoff from tributaries downstream of the dam can cause high water temperatures and low dissolved oxygen levels that are stressful or lethal to developing embryos. Reduced flow may also minimize flushing of inter-gravel waters within nests, allowing buildup of metabolic wastes, exacerbating stressful conditions.


A flow management group that included scientists from California State Water Board, U.S. Fish and Wildlife Service, NOAA Fisheries, City of Sacramento, Sacramento Water Forum, and Cramer Fish Sciences (CFS) developed an emergency monitoring plan to:

  1. Estimate the number and proportion of salmon embryos that were potentially stranded during flow reduction,
  2. Monitor intergravel environmental parameters that are important for embryo survival,
  3. Identify potential mitigation options that also considered societal water needs,
  4. Monitor the effects of management decisions on incubating embryos and rearing juveniles.

Redd dewatering and stranding

To measure the impacts of the reduction on natural LAR Chinook salmon production, Cramer Fish Sciences (CFS) performed assessments of LAR redd dewatering and stranding during and after the four-step flow reduction. All agencies collaborated to conduct fieldwork for this project. To assess dewatering due to reduced flow, we used hand-held Trimble GPS units to map water's edge at each 100 cfs of flow reduction at nine representative locations in each of three reaches of the LAR (see Figure 2). We then used locations of redds based on surveys conducted the previous fall to estimate the number and proportion of redds that were dewatered at each of the sample sites at each 100 cfs flow reduction step (Figure 4). These estimates were extrapolated across the entire LAR to generate an estimate of the proportion of redds and embryos that were dewatered by each flow reduction (Figure 5).

Following the flow reduction, CFS staff and collaborators monitored intergravel conditions on a weekly basis to track water quality parameters, including water temperature and dissolved oxygen. Snorkel surveys were also conducted in potential areas of fry stranding. A recommendation was made to the flow management group for a pulse flow of 1500 cfs based on observations of increasingly stressful intergravel water quality conditions and of stranded fry within the system. We used temperature-based growth models and redd survey data to predict when a high proportion of embryos would be hatched and ready to emerge from the gravel to recommend dates for the increased flow.

A pulse flow was implemented between 9-10 February 2014 to promote embryo emergence and re-connection of partially dewatered redds. Continued monitoring of gravel conditions and stranded redds after the initial flow pulse led to a second flow pulse to approximately 1000 cfs between 6-7 March 2014. The objective of this pulse was to reconnect migration corridors for stranded fry within the gravel and juveniles in off-channel habitats and ameliorate poor water quality parameters. CFS monitored habitat quality and juvenile salmonid abundance (using snorkel surveys, drift sampling, and underwater video) before, during, and after pulse flow events.

Results from this exercise will provide a framework for future water management decisions, as human demands increase and the climate continues to trend toward greater precipitation extremes.

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