Delta Pathways and Outmigrating Salmon Survival Spotlighted

The US Fish and Wildlife Service and a CALFED Science Fellow from the University of Washington have conducted several analyses to assess the survival of juvenile Chinook salmon outmigrating through the lower portions of the Sacramento and San Joaquin Rivers and through the Delta. Both projects were spotlighted during recent CALFED Science Program brown bag seminars.

The main factors studied include migration routes (main stem of the Sacramento River versus interior of the Delta), and water operations parameters (open or closed gates or barriers, export rates, and combinations of export rates and outflows).

Outmigrating salmon from the Sacramento River system are more likely to survive when they remain on the main stem of the river than those that enter the interior Delta through open Delta Cross Channel gates or Georgiana Slough. Fish migrating through the interior Delta are subject to stresses of water export operations, predation and poor water quality conditions. Higher levels of export operations can reverse flows and draw fish into the south Delta pumping facilities. Fish that navigate through the interior of the Delta also have a more tortuous path and take longer to migrate out of the Delta. The longer migration time exposes fish to potential predation and to poor water quality conditions including elevated temperatures and contaminants.

Deficiencies were identified in previous statistical analysis of four tagged salmon outmigration studies, so Dr. Ken Newman, a USFWS statistician, took another look under a Science Program grant, utilizing Bayesian hierarchical models to re-analyze the data. Using this improved approach, Newman could simultaneously analyze recoveries of tagged fish at the western edge of the Delta and from the ocean fisheries while accounting for sampling variation and environmental variation. Here’s what Newman found:

Sacramento River outmigration

  • Juvenile salmon survival is lower when the Delta Cross Channel gates are open, allowing more opportunities for fish to enter the interior Delta. However, a high level of variability was observed in the data. Fish released into Georgiana Slough and migrating to the interior Delta were 15 to 16 times more likely to end up at the salvage facilities of the water export stations than those released in the main stem Sacramento River. The probability of a fish surviving to Chipps Island that had been released into Georgiana Slough was about 65 percent less than the probability of survival for a fish that stayed in the main stem Sacramento River. In addition, there is a weak negative relationship between survival of fish released into the interior Delta and export levels.

San Joaquin River outmigration

  • Survival of fish migrating through the San Joaquin River is higher than that of those migrating through Old River, indicating likely benefits of the Head of Old River Barrier in keeping out migrating salmon in the main stem San Joaquin River. And there is evidence for increasing survival with increasing flows.

Russell Perry, a CALFED Science Fellow, is developing a model to estimate survival probabilities of juvenile salmonids using different migratory pathways through the Delta, and the overall survival probabilities for outmigrating Sacramento River salmon; in other words to try to answer the questions “Where do the fish go? Why do they go there? How well do they survive each pathway? How does that add up to overall survival?”

Perry looked at four outmigration routes: two that keep fish from the interior Delta (main stem Sacramento and Sutter and Steamboat Sloughs) and two that allow fish into the interior Delta (Delta Cross Channel and Georgiana Slough). He determined the fraction that used each route and the survival for each route.

Perry got similar results to the Newman study - survival in the Sacramento mainstem was always higher than survival in the interior Delta. As with the interior Delta routes, survival through the Sutter/Steamboat Slough route was lower than the main stem Sacramento survival December releases, but was identical for January releases.

Perry then analyzed the flow splits at the junction of the Sacramento River, Delta Cross Channel and Georgiana Slough compared to where the fish go. His conclusion is that fish do “go with the flow,” but where fish go is strongly dependent on the flow conditions when fish arrive at the junction. In turn, fish arrival timing varies depending on night/day fish activity and variation in travel times. The models Perry developed are useful for predicting entrainment and survival at the observed flow ranges, which is helpful information for Delta resource managers. His findings can be directly incorporated into management models to better understand how water management actions influence both where fish go and how well they survive through different migration routes.