Delta Water Flows and the Migration of Chinook Salmon Smolts

Cover Photo: Chinook salmon smolt release (Source Pacific Southwest Region of the U.S. Fish and Wildlife Service)

Chinook salmon in the Sacramento-San Joaquin River system (the California Central Valley) begin life by hatching from eggs in high elevation, mountain freshwater streams. In order to complete their life cycle, they must migrate through the Delta to the ocean saltwater and then return to the mountain freshwater streams to reproduce several years later. Groups of Central Valley Chinook salmon are distinguished by the time of year when they return from the ocean to freshwater. Spring-run Chinook have historically been the largest population of Chinook salmon in the Sacramento-San Joaquin River watershed.

The construction of the Friant Dam on the San Joaquin River in 1972 blocked the salmon migration route. In addition, water diversions in the San Joaquin River greatly reduced water flows. The combined barriers of the Dam and the low water flows prevented spring-run Chinook salmon from migrating to higher elevations to reproduce. With these barriers, spring-run Chinook virtually disappeared from the San Joaquin River. Natural populations of spring-run Chinook only remained in a few creeks in the upper Sacramento River watershed.

To support efforts to reintroduce Chinook salmon to the San Joaquin River, in 2016 CDFW funded U.C. Davis to study juvenile Chinook salmon (“smolts”) migration. The study tracks smolts as they migrate from the San Joaquin River, through the Delta, and to the ocean. This research explores the extent that Chinook salmon can successfully navigate through the complex flow dynamics in the Delta to complete their life cycle.

• Project Proponent: University of California, Davis
• Project Partners: Delta Science Program; U.S. Fish and Wildlife Service; CDFW Salmon Conservation and Research Facility; U.S. Geological Survey; California Department of Water Resources
• Focus Habitat/Species: Spring-run Chinook salmon
• CDFW Grant Support: $1,510,723
• Location: Junction of San Joaquin River with Head of Old River in South Sacramento/San Joaquin River Delta
• Scale: San Joaquin River Delta/San Joaquin River
• Timing: 2017 - 2021
• Funding Source: Proposition 1 

Spring-run Chinook in the San Joaquin River

In 1999, spring-run Chinook salmon were listed as threatened under both the state and federal endangered species acts. In 2009, the San Joaquin River Restoration Settlement Act mandated that spring-run Chinook salmon be reintroduced into the San Joaquin River. Since 2013, the San Joaquin Restoration Program has been releasing spring-run Chinook salmon smolts (young salmon that migrate to the ocean) in the San Joaquin River, upstream of the Delta.

Subsequent studies showed that in 2019 the reintroduced spring-run Chinook successfully reproduced in the San Joaquin River. These results verified that some of the reintroduced Chinook salmon were able to pass through the modified flows in the south Delta to reach the ocean, then return to the San Joaquin River to complete their life cycle.

Delta Water Flows and Salmon Migration

In addition to barriers in tributary rivers, such as the San Joaquin River, salmon must pass through altered flows in the Sacramento-San Joaquin Delta. Water flows that occurred in the Delta during the evolution of the Chinook salmon life cycle have been greatly altered by water exports, hydroelectric dams, and sea level rise.

Historically, water flows in the Delta were controlled by freshwater flows from rivers and saline tidal flows. Freshwater inflows were highest in the spring, when rain and snow melt flowed into the Delta. Tidal flows varied with the moon cycle.

Today, flows in the Delta are controlled primarily by the large state and federal pumping facilities located near Tracy, at the southern edge of the Delta. These pumps export vast amounts of water to roughly three million acres of farmland and 25 million Californians south of the Delta.

Water export pumping in the south Delta impacts migratory fish both by trapping them in the pumps and by creating negative flows that confuse fish as to which they should swim 'downstream’ to reach the ocean. Runoff continues to flow into the Delta during the spring, but during the remainder of the year inflows are controlled by releases from large dams upstream of the Delta. In addition, tidal flows are increasingly affected by sea level rise. 

This project aims to describe the swimming movement of spring-run Chinook salmon smolts in the south Delta. The study joins experts from wildlife ecology with hydraulic modellers to examine the response of out-migrating salmonids to varying flow dynamics.

Researchers collected data on fish movement in combination with water flow data from gauging stations over a three year period.  Ultra-miniature acoustic transmitters were attached to fish to track their migration from rivers to the ocean.  

This research focuses on flows in the south Delta in general, and more specifically in the region of the San Joaquin River where the main River splits into the first of two major channels that flow into the Delta. This junction, commonly referred to as the Head of Old River, is of significant interest to resource managers, research biologists, and state and federal water operators. 

An array of receivers were used to record the fish transmitter signals as fish swam past the Head of Old River junction. Additional receivers were installed further downstream to track the continued migration of fish through the Delta toward the ocean. Researchers combined data on fish movement with water flow data to determine the extent that fish are passively transported by flow currents, as opposed to actively swimming toward a destination.

The study is providing data regarding flow, water export pumping, and juvenile fish survival. After testing the results, researchers plan to scale the results up into large-scale models to estimate the location of young salmon in the Delta based on flows and season. Researchers will use modelling to estimate the number of juvenile salmon routed or lost due to mortality in channels of the south Delta. 

Model results will also allow for travel time predictions for fish migrating through the Delta and into the San Francisco Bay. The work will serve to explore alternative management scenarios that could improve survival of migrating fish in the Delta and aide in recovery of ESA listed spring-run Chinook salmon.

For more information see: 

• To see other Project Highlight StoryMaps like this one, see:  https://www.wildlife.ca.gov/Conservation/Watersheds/Project-Highlights 
• For Information on Proposition 1/68 Projects, please see:  https://www.wildlife.ca.gov/Conservation/Watersheds/Restoration-Grants/Projects 
• For further information, please contact:  WatershedGrants@wildlife.ca.go v