US Army Corps of Engineers Research Project

Juvenile salmonid outmigration studies in San Francisco Bay

Information on the temporal and spatial distribution of Federally-listed juvenile Chinook salmon and steelhead in San Francisco Bay is needed for assessing potential impacts to these species from dredging and dredge material disposal activities. Currently, environmental windows limit these activities to periods of time when listed salmonids are thought to be absent from the bay. Through the use of hydroacoustic telemetry we hope to increase our knowledge of juvenile salmonid migratory behavior in order to better manage dredging projects. Through a collaborative multi-agency effort, 400 Chinook salmon smolts and 250 steelhead smolts implanted with ultrasonic tags will be released each year during the winter months of 2007-2009. As the smolts move from the Sacramento River, through the Estuary, and under the Golden Gate Bridge during their outmigration, they will be detected by hydrophone monitors. Monitors will be strategically placed in order to better define juvenile salmonid migratory routes, transit times, and distribution in the vicinity of dredging and dredge disposal sites; thus providing the information needed to make well-informed decisions regarding dredging and dredge disposal, as well as potential other water-related activities.

The project has three specific technical objectives:

  1. Estimate transit rates of juvenile steelhead and Chinook salmon between the Carquinez Strait, the Richmond-San Rafael Bridge, and the Golden Gate Bridge during outmigration.
  2. Obtain better information regarding locations and habitat types used during outmigration.
  3. Document the temporal occurrence of the two fish species during outmigration.

We will surgically implant ultrasonic transmitter tags into the peritoneal cavity of 50 late fall run Chinook smolts and 50 steelhead smolts. The smolts, acquired from the Coleman National Fish Hatchery (CNFH) in Anderson, CA, will be transported to the Center for Aquatic Biology and Aquaculture (CABA) in Davis, CA. After a holding period of one week, 10 fish of each species will be tagged and held for five days. On the fifth day, the tagged fish and 100 “escort” fish will be released into the Sacramento River in Rio Vista, CA; 10 more fish of each species are tagged the same day, and then held for five days. This procedure continues until all of the fish are released. The release dates are spaced out so we can compare the effect of environmental variables on movement; help decrease the potential for “tag collisions” (failure of detection due to multiple pinging at a monitor); and minimize the effects of predation. Monitor sites in the San Francisco Estuary include: curtain arrays at the Richmond-San Rafael Bridge, the Golden Gate Bridge, and Raccoon Strait; two sets of channel markers in the San Pablo Bay; two dredge material disposal sites; the mouth of the Petaluma River; and a dredging site at the Richmond Harbor. Monitor downloading will begin 30 days after all fish are released, and will continue until monitor data indicate zero detections. This research will be conducted for a minimum of three years.

We have deployed all monitors at the sites listed above. Salmonid tagging has been completed for the 2007 season, and all tagged fish have been released. We are currently interrogating the monitors at all sites and have had success with locating, retrieving, and downloading data from the monitors (with the exception of the array in Raccoon Strait, which has very strong flows), and should have all of the tag detection files in hand within the next few months. We will be adding tag detection files to the database and will make them available on the web page.