The fish fauna in the Monterey Bay National Marine Sanctuary constitute a diverse and significant ecological resource. There are at least 345 fish species distributed across a wide variety of habitats in the sanctuary, with each habitat having its own characteristic fish assemblage.

The sanctuary is located at the southern end of the range of many species that are part of the very diverse, cold-temperate fauna that make up the Oregonian province. Occasionally, southern species from the California Province (south of Point Conception) extend their ranges to central and northern California during warm oceanographic events, such as El Niño and the Pacific Decadal Oscillation.

Conservation and management issues affecting fishes in the sanctuary include fisheries, habitat loss and alteration, productivity, and oceanographic conditions.

• Fisheries: The diverse fisheries in central California are part of the region's rich cultural and economic history. The sanctuary does not currently manage commercial or recreational fisheries; the Pacific Fishery Management Council and California Department of Fish and Game manage federal and state fisheries, respectively.

• Habitat: Trends for two habitat types, where similar species groups are caught, can be described:
  • Soft-bottom deep-shelf and soft-bottom slope are the two most prevalent habitats in the sanctuary. They contain mud and silty sediments and a large number of invertebrate species. A combination of regulations (for rockfishes and flatfishes) and environmental conditions (affecting Pacific Ocean shrimp and Dungeness crab recruitment) led to a recent decline in catch in this habitat group.
  • Semipelagic rockfishes are the primary component of catches in rocky deep-shelf and rocky slope habitats. These habitats are usually characterized by high-relief rock pinnacles, boulders or walls. Overall commercial catch trends within the sanctuary (1981 to 2000) of all species from rocky deep-shelf and rocky slope habitats reflect the general declining population trend of many rockfishes. For more information on the trends of fishes caught, see http://www.sanctuarysimon.org/regional_sections/fisheries/overview.php?sec=f.
  Habitat loss and alteration from human activities is of special concern. Some habitats are critical for certain life stages of species, such as spawning or rearing. The habitats in this region that are most threatened include estuaries and coastal wetlands, eelgrass and kelp beds, and rocky bottoms.
• Productivity and Oceanographic Conditions: Many organisms, including some fishes, depend on ocean currents for larval dispersal and recruitment. Therefore, the variability of oceanographic features and events (e.g., upwelling, El Niño), affects fish populations. Rockfishes (genus Sebastes), for example, exhibit extreme variability in reproductive success.

Monitoring

A number of scientists in this region are working on monitoring programs to study fishes in the various sanctuary habitats. These programs include monitoring the natural variation of fish abundance in kelp forests; studying the influence of tidal exchange on the fishes in Elkhorn Slough; characterizing groundfishes in deep, rocky-shelf habitats; and surveying the distribution and abundance of pelagic juvenile young-of-the-year rockfishes.

Some of these programs are described below.

The Influence of Varying Tidal Exchange on the Fish and Crab Assemblages of Elkhorn Slough
Scientists from Elkhorn Slough National Estuarine Research Reserve and UC Santa Cruz investigated how assemblage structure and species distribution and abundance patterns of fishes and crabs are influenced by variation in tidal flow and freshwater input throughout shallow-water habitats in the Elkhorn Slough estuary.

Fish and crab abundance patterns were surveyed throughout 18 locations in Elkhorn Slough that fall into one of three categories: full tidal flow, muted tidal flow and very muted tidal flow/seasonally high freshwater input. Fish and crab abundance patterns varied across habitat types and across seasons, depending upon which species were considered. The very muted/seasonally high freshwater input sites were most different in terms of species composition and abundance patterns compared to the other two flow regimes, but there were also differences between the full and the muted flow sites in regards to these factors.

Long-term Monitoring of Groundfishes in the Monterey Bay National Marine Sanctuary
In 2004, scientists from California Sea Grant, California Academy of Sciences, NOAA Fisheries, Moss Landing Marine Laboratories and the sanctuary surveyed deep, rocky continental shelf habitats to characterize, monitor and assess long-term changes in benthic fishes and associated habitats. They conducted 131 visual strip transects aboard the submersible Delta to compare groundfish abundance, size and diversity off Monterey Peninsula and Point Sur from 70 to 120 meters.

Overall species diversity, abundance and sizes were greater off Point Sur than off the Monterey Peninsula. Off the Monterey Peninsula, the deeper (70 to 90 meters) high-relief rocky areas had lower species diversity than the shallower (90 to 120 meters) low-relief areas.

The scientists also revisited sites off Monterey Peninsula that were surveyed in 1993 and compared abundance, species-habitat relationships, and species and size composition. Species composition was relatively similar. Mean lengths of all rockfishes were greater in 2004 than in 1993, except for yellowtail rockfish, Sebastes flavidus, and squarespot rockfish, Sebastes hopkinsi.

Trends in Fisheries and Fishery Resources
A recent study by scientists at California Sea Grant and Moss Landing Marine Laboratories summarized trends in fisheries and fishery resources associated with the sanctuary from 1981 to 2000.

More than 200 invertebrate and fish species are commercially or recreationally harvested from sanctuary waters, with the bulk of the commercial landings composed of squid, rockfishes, salmon, albacore, Dover sole, sablefish, mackerel, anchovy and sardines. A decline in commercial landings at sanctuary ports from 1981 to 2000 was directly related to reduced population sizes of many of the species inhabiting deep-water bottom habitats, caused by excessively high rates of fishing in the 1980s, when fishery scientists and resource managers overestimated the productivity of bottom fish stocks.

From 1990 to 2000, catches of many fishery resources greatly declined, due both to decreases in fish populations and to new regulations enacted to conserve or rebuild fish stocks.

Mid-Water Trawl Pre-Recruit Survey
The productivity of rockfish (genus Sebastes) fisheries depends almost exclusively on the occurrence and influx of strong year classes. Sound management of these fisheries, therefore, requires accurate information on impending recruitment.

During May and June every year since 1983, the NOAA NMFS SWFSC Fisheries Ecology Division has performed an annual survey of the distribution and abundance of pelagic juvenile young-of-the-year (YOY) rockfishes aboard the NOAA Ship David Starr Jordan. YOY rockfish catches showed a large degree of temporal variability. In addition, the temporal patterns were similar among many of the different rockfish species. Catches were generally large during the 1980s but dropped substantially during the 1990s, with the exception of 1991 and 1993.

The poor catches during the 1990s could be attributed to the generally warm conditions during that time period as well as the occurrence of strong El Niño and La Niña conditions, which adversely affect rockfish recruitment. Generally cooler ocean conditions began to develop beginning in 2000, and YOY rockfish catches increased substantially from the very low catches of 1998 (an El Niño year), with large numbers collected during 2002 and 2004. However, since 2004, catches north of Point Conception have been very low. In 2005, in the area south of Point Conception, catches of YOY rockfish were extremely high, indicating significant environmental/ecological differences between the regions north and south of Point Conception.