Plants, Wildlife, and Fish

From red-tailed hawks and mountain lions on the slopes of Mount Tam to oysters and harbor seals in the bays and on the coast, a diversity of wildlife inhabits Marin County.  The fish, birds, mammals, reptiles, amphibians, and invertebrates that live here depend on healthy watersheds to survive.


No creatures are more symbolic of healthy watersheds than native fish--and in our region, no fish are more indicative of healthy watersheds than coho salmon and steelhead. These salmonids are anadromous fish; they are born and rear in freshwater streams, migrate to the ocean to grow and mature, and return to freshwater to reproduce. Historically, many Marin County creeks supported these fish, but the numbers of native coho and steelhead have dropped dramatically in recent decades.  Coho in particular have disappeared from many of the streams they once inhabited. In west Marin, Chinook salmon, also an andromous fish, are also observed consistently in the Lagunitas Creek system.

The life cycles of coho salmon and steelhead have many similarities, although the precise schedule, microhabitat requirements, and the amount of time spent in freshwater and the ocean varies. Coho salmon spend their first year in freshwater creeks, migrate to sea where they mature for two years, and return to their native creek to spawn and die. Steelhead have a similar life cycle, but they live in freshwater for one to two years, spend one to four years at sea, and return to spawn as many as four times.  Life cycle and migration timing make steelhead more resilient to change, but both coho salmon and steelhead have relatively specific habitat needs, including:

  • A year-round supply of cool, clean water;
  • Diverse habitat with deep, quiet pools and shallow rocky areas (riffles);
  • Clean spawning cobble and gravels without fine sediment;
  • Relatively stable creek banks;
  • Dense shade canopy from creekside vegetation, to cool water, provide insect habitat, and contribute nutrients;
  • A supply of woody debris from fallen trees and branches;
  • Adequate food supply—primarily insects; and
  • An abundance of cover—undercut banks, rocks, tree roots, surface turbulence, overhanging creekside vegetation, deep quiet pools, and woody debris—for refuge from predators and heavy storm flows. 1

Urban development in our watersheds can disrupt the natural processes that create these habitat qualities.  Increases in paved areas and loss of riparian vegetation can lead to more intense stormflows and simplified stream channels which make it hard for sensitive fish species to survive. Runoff of chemicals from roads, yards, and industrial areas degrades water quality.  Channelized reaches of creeks, lined with concrete, offer little habitat value.  In many places dams and culverts limit fish passage. However, intact baylands, streams running through the valley floor, and upland headwaters still provide critical habitat for fish.

Many other species of fish also inhabit Marin County’s streams, marshes and bays. Common native freshwater species include California roach, threespine stickleback, Sacramento sucker, and prickly sculpin.  The eelgrass beds of Richardson and Tomales Bays are especially rich in fish species.  California bat ray, leopard shark, Pacific herring, and northern anchovy are just a few of the many species documented in these rich tidal baylands.  

The University of California maintains a website of California fish.

Reptiles and Amphibians

Marin County’s amphibians and many of its reptiles utilize upland terrestrial habitats and are also dependent on the condition of creeks and riparian habitat during a portion or all of their life stages.

Many amphibian species require diverse, healthy riparian vegetation, good water quality and quantity and structural diversity to survive. Pacific giant salamanders breed in streams and need shady streambanks and woody debris for protection. The California red-legged frog, a threatened species, forage and breed in ponds and streams where emergent plants such as sedges and rushes provide cover and nesting substrates. Special-status northwestern pond turtles live in or near ponds or slow-moving creeks and need suitable rocks or logs for basking sites and underwater retreats. Adaptable Pacific tree frogs utilize streams, ponds, moist woodlands, and developed areas for breeding and year-round habitat.  Foothill Access to adjacent upland habitat or corridors for movement up and downstream is essential for many wildlife species, including amphibians that live in upland habitats but must move to aquatic habitats to breed.  For example, California red-legged frogs and California newts make their way from upland habitats to ponds or slow-flowing streams to breed. Foothill yellow-legged frogs, a close relative of the California red-legged frog, also utilizes perennial, rocky stream; however, it is never found far from water.

Reptiles including snakes and lizards can be found throughout the upland, valley floor, and bayland habitats. Much less depended on stream corridors, they utilize a variety of habitats. Common reptiles including gopher and garter snake, western fence lizards and alligator lizards can be found anywhere from urban valley floors to ridge tops grasslands.


Over 150 species of birds live and breed in Marin County, including a number of rare and threatened species.  These birds rely on watershed features such as mature riparian trees and snags for roosting and nesting; plentiful fish, amphibians and other small animals for food; and natural tidal flows to maintain rich coastal marsh habitat.

An extraordinary abundance of birds lives in Marin County’s coastal baylands.  The endangered California clapper rail inhabits coastal salt marshes, feeding on invertebrates.  The clapper rail builds its nests on or near the ground in dense marsh vegetation such as pickleweed, cord grass, and gumplant.  The threatened California black rail is usually found in brackish marshes with unrestricted tidal flow where dense cover is available to protect from predation by enemies. The black rail weaves its cup-shaped nest in tall grasses or marsh vegetation.  Hundreds of thousands of other shorebirds and waterfowl migrating along the Pacific Flyway stop for the winter in Richardson Bay, where eelgrass beds provide rich feeding grounds, and the rich feeding grounds of Tomales Bay.

The upland dense redwood-fir forests support the threatened northern spotted owl, at the southern limit of its range.  Spotted owls inhabit forests with multi-layered canopy cover, using natural cavities or platforms of branches in mature or standing dead trees as nests.  Woody debris on the forest floor provides habitat for the mice, voles, and other small mammals that the owls hunt. Oak woodland habitats provide important habitat for the acorn woodpecker, a highly sociable bird that utilizes dead and dying trees to cache acorns. Its raucous call can be heard throughout the county.  

The riparian corridors of Marin’s lower hills and valleys support some of our more familiar bird species. Red-tailed hawks build nests of sticks, twigs, bark, mosses, and other materials in mature trees along forested drainages.  They hunt a variety of small animals such as snakes, frogs, and rodents. California quail nest on the ground in dense vegetation near streams or other water sources.  The Swainson’s thrush, with its unique upward-spiraling song, can often be heard in well-vegetated riparian habitats.  These birds build their nests in low branches or crotches of willows. They mix leaves, twigs, and mosses with mud to fashion their nests, lining them with dry grasses and other fine plant matter.  Great blue herons, great egrets, and snowy egrets nest in colonies high in large firs, bays, oaks, and eucalyptus, often near shallow water foraging grounds where they stalk fish, crustaceans, and other small animals. Tree swallows frequent riparian corridors and surrounding woodlands, utilizing old tree snags and excavated cavities for nesting, as do wood ducks.


Riparian habitat often serves as essential wildlife corridors between habitat patches in an otherwise fragmented, urbanized landscape.  For many animals, it is not only the quality of one patch of habitat, but also the ability to move among multiple habitat patches for example from uplands through the valley floor, that makes survival possible.  Mountain lions, black-tailed deer, coyotes, and other Marin County mammals must be able to move to survive.  Large predators such as the mountain lion need to range widely to find sufficient prey.  Black-tailed deer and other herbivores must follow shifting food sources as vegetation changes with the seasons.  Many mammals such as coyotes disperse from their initial home range to establish their own territories before reaching maturity.

On a much smaller scale, the endangered salt marsh harvest mouse (weighing a little less than a nickel) also needs a variety of connected habitat types.  This tiny mouse occurs only in San Francisco Bay area salt marshes.  It eats the seeds and stems of salt marsh plants and builds ball-like nests on the ground or in pickleweed. Intact salt marsh habitat typically consists of three broad zones, shaped by the level of inundation and salinity at different elevations. Cordgrass usually dominates the lowest zone; pickleweed occurs in the middle; and a variety of salt-tolerant plants, such as saltgrass, occupy the marsh edges, which then transition into grassland. As tides rise, the salt marsh harvest mouse must move up and inland from its favored pickleweed zone.  In our region, though, most marshes have lost the broad upper edges that could provide refuge. Upper salt marsh zones have been developed, filled, or reshaped into steep levees.  This leaves no place for the mouse to go during high tides.  Hydrologic changes resulting from groundwater pumping and discharge of non-saline sewage are also thought to diminish the pickleweed zone, restricting the salt marsh harvest mouse even further.


Freshwater aquatic invertebrates are an important food source for many of our more “charismatic” wildlife species like coho and steelhead.  They are also valuable as indicators of watershed conditions.  The species and numbers of aquatic invertebrates present in a stream reveal information about water quality and riparian conditions. Because aquatic invertebrates are relatively easy to collect and vary distinctively in their tolerances for aquatic pollution, biologists often analyze them to understand habitat conditions limiting salmonids.  For instance, larvae of stoneflies, mayflies, and caddisflies are important prey for fish and their presence usually reflects healthy creek conditions. Water boatmen, water striders, dragonflies, and water beetles are other common inhabitants of Marin County streams.

Marin County is also home to several rare invertebrates.  The endangered California freshwater shrimp occurs only in a handful of creeks in Marin, Napa, and Sonoma counties.  This species is adapted to low to moderate gradient streams which are well incised and support relatively dense stands of mature riparian tree vegetation.  It feeds on decomposing plants; and avoids predators, and the high velocity flows that occur during winter storms, by hiding under overhanging banks and among submerged tree roots. Its variable color pattern, ranging from nearly transparent to a dark brown, helps it escape detection.  The original distribution of the California freshwater shrimp is largely unknown, but it has probably disappeared from many streams because it cannot survive in creeks that have been straightened or channelized, in creeks where banks have been denuded, or where water diversions have diminished stream flows.

Marine invertebrates are abundant in Marin County’s bays and along the coastline. These include edible native species such as California oysters, red abalone, native clams, and Dungeness crabs.  Some of these species are declining; the causes of this decline are complex and include over-harvesting and pollution from mainland sources.  High levels of nutrients, sediment, pathogens, and persistent toxic chemicals are known to occur in some of Marin County’s bays and coastal waters and may be contributing to the declines.


1 Text on salmonid habitat needs adapted from Creek Care: A Guide for Marin Residents, Marin county Stormwater Pollution Prevention Program, 2009.