Sanctuary Integrated Monitoring Network
Monitoring Project

Coastal Ecology of Juvenile Salmonids in California

Principal Investigator(s)

  • Bruce MacFarlane
    NOAA Fisheries
Start Date: January 01, 1998

Salmonid stocks (chinook salmon, Oncorhynchus tshawytscha, coho salmon, Oncorhynchus kisutch, and steelhead, Oncorhynchus mykiss) from California’s Central Valley and coastal streams continue to decline. All four of California’s Central Valley chinook runs are either listed or candidates for listing by the Endangered Species Act. Coastal chinook , coho, and steelhead evolutionarily significant units are likewise imperiled.

Although freshwater habitat loss and degradation contribute to population declines, it is becoming apparent that ocean conditions play a major role in the interannual variability in salmon biology, especially during the first months after exiting freshwater. Climatic and oceanographic physical forcing, on temporal - spatial scales ranging from interdecadal whole-ocean to interannual mesoscale to seasonal localized phenomena, affect marine productivity and environmental conditions that influence salmon growth and survival.

Effective management of salmonid stocks and their ecosystems requires greater knowledge of the abundance, distribution, growth, health, and ecology of juvenile salmonids during marine residence. The need for basic biological data and the influences of environmental factors on survival and health have been identified as high priority research needs by the Pacific Fishery Management Council (Research and Data Needs 1998-2000, PFMC, September 1998) as well as the scientific community (Estuarine and Ocean Survival of Northeastern Pacific Salmon, Proceedings of the Workshop, April 1997; NMFS Estuarine and Ocean Salmon Strategic Research Plan, April 1998).

Implicit in these needs is the ability to distinguish separate populations, including those of natural and hatchery origins, and to differentiate the influences and consequences of ocean and freshwater processes on individual stocks. The results of the proposed study will help focus conservation and management efforts on the most cost-effective options for this socio-economically valuable resource. Additionally, essential salmonid habitat (e.g., areas of abundance, intense feeding, etc.) in coastal ecosystem will be identified.

The goal of this study is to determine the abundance, distribution, growth, and health of juvenile salmonids and the influences of environmental factors on the central California coast. Specific objectives are to determine seasonal abundance and distribution, movement patterns in the ocean, salmonid association with oceanographic features (fronts, jets, upwelling centers, eddies), growth, age, maturation, energy status, immune status/pathology, species, stock, origin (natural/hatchery) identification, trophic relationships (plankton, forage fish), predation (marine mammals), associated fish communities, relationships between environmental conditions (primary and secondary productivity, temperature, salinity, hydrodynamics [upwelling, currents], and meteorology) and salmonid biology.

Summary to Date

After ocean entry (June-August), most subyearling chinook salmon remain in the Gulf of the Farallones; a portion proceeds north on the continental shelf. Northward distribution on shelf increases as season progresses (September-November). Greatest CPUEs occur at an eddy north of the Golden Gate and at a coastal jet south of the Golden Gate. There is no evidence of extended southward movement by subyearling chinook salmon.

Mean daily otolith increment widths for subyearling juvenile chinook salmon captured in the Gulf of the Farallones in the fall of 1998 and 1999. There was no significant difference in ages of samples between the two years. Increment widths were greater in the 1998 El Nino period than in the 1999 La Nina. N = 10 for each year. Prey primarily small fish, decapod and euphausiid early life stages, amphipods.

Subyearling chinook salmon grew faster during 1998 El Nino than 1999 La Nina. Microchemical analysis of juvenile portion of adult otolith shows promise as a tool to determine stream of origin; microstructural analysis allows determination of hatchery or wild origin.

Study Parameters

  • Abundance
  • Distribution
  • Migration/movement patterns
  • Habitat
  • Growth
  • Age & Growth
  • Mortality
  • Genetics
  • Trophic association
  • Predation
  • Temperature
  • Salinity
  • Upwelling/downwelling
  • Tagging
  • Stock assessment
  • Sex ratio

Study Methods

Incorporate environmental data (e.g., current profiles, freshwater outflow, temperature, salinity, upwelling indices, sea level data, AVHRR and CZCS image data, barometric pressure, rainfall, wind) from other governmental and academic sources.

Obtain environmental data (CTD data - depth profiles of temperature, salinity, PAR; current profiles) concurrent with salmon surveys.

Survey and collect salmonids along California coast by trawl during period of ocean entry (March - June), after short residence (September - October), and during period of lower prey abundance (February-March). Survey by a series of transects from Pt. San Pedro to Ft. Ross between 15 and 100 fathoms depth and in association with oceanographic features (fronts, upwelling centers, jets, eddies).

Tag representative salmon with archival tags to record movement history (record depth and temperature by time).

Determine growth history by otolith analysis.

Assess sex, length, weight, maturation state, physiologic condition (tissue morphometrics, Goede's and Adam's health assessment evaluations), energetic and nutritional status (lipid class and protein analyses).

Determine immunocompetence and/or pathological state.

Analyze species and size-stratified stomach contents (quantity, prey species composition and dominance).

Estimate salmon predation by seals and sea lions by analysis of stomach contents using visual and genetic analysis.

Establish stock/run identity of individuals by genetics, microchemical otolith analysis, tags/fin clips.

Estimate primary productivity (calibrated vertical and horizontal fluorometry, CCS satellite imagery) and zooplankton and neuston abundance and speciation.

Assess forage fish and fish community coincident with juvenile salmonids (identify and enumerate species captured during salmonid collections).

Integrate salmonid data with biotic and abiotic environmental data to determine variables affecting salmonid biology and other interrelationships.