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Cramer Fish Sciences: Stanislaus River Survival Study   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: Stanislaus River Survival Study




Assessment of juvenile Chinook Salmon survival and outmigration behavior in the lower Stanislaus River using radio telemetry.

In spring 2012-2014, Cramer Fish Sciences (CFS) conducted a multi-year mark-recapture experiment funded by the U.S. Fish and Wildlife Service (USFWS) Anadromous Fish Restoration Program (AFRP: Grant #81332BG003) to estimate survival of radio-tagged juvenile Chinook Salmon Oncorhynchus tshawytscha emigrating through the lower Stanislaus River (LSR) between the Oakdale Recreation Area rotary screw trap (RST) located at river km (rkm) 64.4 and the Caswell Memorial State Park RST located at rkm 14.4. A series of paired releases were performed along the approximately 50-km study reach in six roughly equal sub-reaches. The two releases were performed about a month apart to examine survival under different flow regimes. Mobile telemetry was performed to monitor daily movements (for up to 14 days following release) and outmigration behavior of experimental fish in relation to potential mortality sources (e.g., predator pools, agricultural diversions, etc.). Each year, additional fish were tagged and observed in a laboratory setting to assess post-surgery survival, tag retention, and behavioral effects of implanted tags.

Site study location

Location of the Stanislaus River in California. The survival study took place along an approximately 50 km stretch between the Oakdale Rotary Screw Trap (RST) and the RST at Caswell Memorial State Park.

The LSR is part of San Joaquin River system, located in California's Central Valley, which once supported escapements of adult Chinook Salmon numbering in the hundreds of thousands of fish (Yoshiyama et al. 2001). The LSR is the stretch of the Stanislaus River below the Goodwin Dam. These historic runs exhibited a rich ecological diversity, and Chinook salmon were present throughout the river system year-round due to broad variation in life history strategies. However, since the construction of New Melones Dam in 1979, the LSR has changed from a dynamic river system, characterized by depositional and scour features, to a relatively static and entrenched system (Kondolf et al. 2001). In addition, dredged channels and mine pits located in reaches below Oakdale reduce flow turbulence and velocity; it has been hypothesized that this affects juvenile salmonids by reducing dissolved oxygen concentrations, increasing travel times, and providing favorable habitat for predators. Reduced dissolved oxygen may contribute to juvenile and adult salmonid mortality when water temperatures are unsuitably warm in late spring and early fall. Increased travel times for juvenile salmonids passing through areas with high predator concentrations in slow flowing channels lacking cover may also foster high rates of juvenile mortality.

Since the early 1990's, rotary screw trapping of juvenile salmonids has been conducted at two locations on the Stanislaus River. The rotary screw trap (RST) located at river km (rkm) 64.4 near Oakdale, CA is downstream from most spawning habitat and provides a measure of juvenile salmon production, whereas the downstream RST, located at Caswell State Park (rkm 13.8), serves to estimate numbers of outmigrating juveniles and provides an indication of rearing conditions relative to production from spawning grounds (see figures below). Data collected over a 17-yr period (1996-2012) indicate a long-term difference in numbers of juvenile abundance at each location, with consistently lower juvenile abundance estimates at the downstream Caswell RST. The reason for the apparently low juvenile Chinook salmon outmigration success remains unclear. Although Kondolf et al. (2001) speculated that predation was a key-contributing factor, it is not known whether survival is constant throughout the migration corridor or if reaches with specific habitat attributes (e.g., in-channel mine pits, agricultural diversions or returns) contribute disproportionately to losses. To better assist AFRP in planning restoration activities, it is important to determine whether mortality is spatially distributed within the migratory corridor, and if so, identify specific locations where the losses occur.

CFS employee tracking radio tagged juvenile Chinook salmon on the Stanislaus River.


This study was designed to provide a scientifically robust and practical assessment of juvenile Chinook Salmon survival within the LSR migratory corridor over several seasonal (e.g., late winter versus spring), flow (e.g., high versus low), and population (e.g., migration timing, size) conditions. The primary goal was to identify sources of mortality and help inform fisheries management and planning efforts that aim to rehabilitate LSR salmonid populations. Consistent with AFRP goals and objectives for Central Valley salmonids, we designed our project to address the following study questions:

  1. Does the survival of salmonid juveniles differ among LSR sub-reaches and migration periods?
  2. What is the distribution of locations with high salmonid mortality throughout the study area and LSR sub-reaches?
  3. How does speed of outmigrating juvenile Chinook Salmon affect survival?
  4. How do biotic and abiotic characteristics affect salmonid survival throughout the study area and LSR sub-reaches?

Schematic of the three study reaches within the study area between the Oakdale Rotary Screw Trap (RST) and the RST at Caswell Memorial State Park. This shows the location of potential mortality sites for juvenile salmonids along the study reach.

Although estimation of survival probabilities and identification of areas exhibiting high juvenile mortality are the primary goals of this multi-year study, we also seek to describe other aspects of juvenile migration, including travel times and migration speeds, which are important for making informed resource management decisions. We also look to compare mortality hotspots to known predator pools and other potential sources of juvenile mortality (e.g., drain returns).


In each year of the study, CFS and collaborators surgically implanted radio transmittal tags into juvenile Chinook Salmon, making sure the tag to body weight ratio was less than 5% (Adams et al. 1998; Brown et al. 1999, 2010), which required a minimum body weight of 5.0 g corresponding to a minimum size between 75-80 mm fork length.

Fish were released at 5-mile intervals throughout the study reach; releases were conducted at night to reduce predation during the release event. These tags allowed tracking of outmigration using both fixed and mobile receivers for up to 21 days after the fish were released. This locational data provided information on outmigration speed, directional movements, geographical and environmental differences in survival, and detection probabilities.

[left] CFS employees surgically implanting radio tags into juvenile salmonids.
[center] Click on this image to view the stages of radio tag implantation.
[right] Group of post-implantation Chinook Salmon with transmitter antennae in the recovery tank. Along with released fish, further tests were done to examine post-surgery survival, tag retention, and behavioral effects of implanted tags.

[Click each picture to view in high resolution]

CFS also collected temperature and river flow data throughout the study, as it is known that changes in temperature and flow conditions affect maturation and survival of developing fish (Embody 1934; Bailey and Evans 1971; Tang et al. 1987; Brandes and McClain 2001; Perry et al 2010).


The final tracking portion of the study was completed in May 2014. Stay tuned to find out how quickly Chinook Salmon outmigrate in the Lower Stanislaus River, what factors affect survival, and how this information can help inform management decisions.

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