Throughout their distribution, California clapper rails occur within a range of tidal and brackish marshes (Harvey et al. 1977). In the south and central San Francisco Bay, and along the perimeter of San Pablo Bay, rails typically inhabit tidal marshes dominated by Sarcocornia pacifica and Spartina foliosa, especially where significant habitats exist that are accessible during high tide. Spartina dominates the lower marsh zone (marsh plain) throughout the south and central Bay (DeGroot 1927, Hinde 1954, Harvey 1988). Sarcocornia dominates the middle and sometimes upper marsh zone throughout the south and central Bay, with Distichlis spicata, Jaumea carnosa, Frankenia salina (alkali-heath), and others mixing with occasional Sarcocornia in the high marsh zone. Grindelia stricta var. angustifolia occurs along the upper edge of tidal sloughs throughout the entire San Francisco Bay Estuary. The marshes of Humboldt Bay, Morro Bay and Elkhorn Slough historically have not supported Spartina. Vegetation at these locations has been dominated by Sarcocornia pacifica and Distichlis spicata (U.S. Fish and Wildlife Service 2013).

Rail foraging and refugial habitat encompasses the lower, middle and high marsh zones, as well as the adjacent transitional zone. Lower and middle marsh zones provide foraging habitat at low tide. Small tidal channels (i.e., first- and second-order) with dense vegetation covering the banks are particularly important habitat features (Keldsen 1997, Garcia 1995). These provide important foraging habitat and hidden routes for travel in close proximity to nesting habitat. Within tidal marshes in portions of north San Francisco Bay, the abundance of California clapper rails is positively correlated with channel density or the total length of channel per unit area of marshland (Garcia 1995, Evens and Collins 1992, Collins et al. 1994, Foin et al. 1997). Keldsen (1997) found that rails prefer locations with a greater number of tidal creeks, Grindelia shrubs and higher elevations. However, high tide conditions result in increased predator pressure on rails in a high marsh zone that has already been reduced by decades of developmental pressure. Sea level rise is expected to increasingly threaten California clapper rail tidal marsh habitat extent and condition (U.S. Fish and Wildlife Service 2013, Zhang and Gorelick 2014, Rosencranz et al. 2018, Thorne et al. 2018, Thorne et al. 2019).

Clapper rails have a wide variety of calls, although few are commonly heard. All calls are variants on a single note, with differences due to changes in intensity, pitch, note length and interval between notes. Massey and Zembal (1987) grouped clapper rail vocalizations into eight calls, of which four are commonly heard: clapper, kek, kekburr and agitated kek. The clapper is the basic species call, serving as a territory pronouncement and for mutual mate recognition. Both sexes clapper year-round, with daily peaks at dawn and dusk (U.S. Fish and Wildlife Service 2013).

The California clapper rail is one of the largest species of the genus Rallus, measuring 32-47 centimeters (13-19 inches) from bill to tail (Ripley 1977).

Males generally weigh 300-350 grams (0.66-0.77 pound) and females 248-301 grams (0.55-0.66 pound; Taylor 1996).

The clapper rail has a hen-like appearance, with a long, slightly downward curved orange bill, a reddish brown breast, black and white barred flanks, and white undertail feathers. Juveniles have a paler bill and darker plumage, with a gray body, black flanks and sides, and indistinct light streaking on flanks and undertail feathers. Downy young are black with dark legs (Eddleman and Conway 1998).

The clapper rail is an omnivore with a relatively broad feeding niche. Animal matter has been consistently emphasized as a major component of the diet (Moffitt 1941, Heard 1982, Zembal and Fancher 1988). Food items found in California clapper rails' stomachs include introduced ribbed horse mussel (Ischadium demissum), spiders (Lycosidae spp.), clams (Macoma balthica), yellow shore crabs (Hemigrapsus oregonensis), amphipods (shrimp-like crustaceans), Nereis vexillosa (a polychaete worm) and striped shore crab (Pachygrapsus crassipes; Williams 1929, Applegarth 1938, Test and Test 1942, Varoujean 1972). Rails occasionally have been seen capturing and consuming rodents, particularly during higher tides; small birds are also occasionally taken (Spendelow and Spendelow 1980, Jorgenson and Ferguson 1982).

Clapper rails are secretive and difficult to observe (U.S. Fish and Wildlife Service 1984). Rails prefer to walk or run over other forms of locomotion, and they swim well (Sibley 1955. Ripley 1977, Todd 1986). When flushed, they normally fly only a short distance before landing (Zucca 1954).

Clapper rails are active for 75 to 90 percent of the day. Activity peaks in the early morning and late evening (Zembal and Massey 1983, Zembal et al. 1989), when rails forage in the marsh vegetation. Rails often roost at high tide during the day (Zembal et al. 1989).

They exhibit strong territorial defense, particularly during the late winter and early breeding seasons (Williams 1929, Albertson 1995, Garcia 1995). Territoriality weakens during extreme high tides when cover is limited, and during the post breeding season (U.S. Fish and Wildlife Service 2013). Clapper rails generally exhibit strong site fidelity (Albertson 1995).

A banding study in the mid-1980s revealed movement of rails in the south Bay of about 500 m (1,641 ft) from the original capture site (U.S. Fish and Wildlife Service 2013). Longer distance dispersal has also been documented, with a female rail moving 2.1 kilometers (1.3 miles) over three days (Albertson 1995) and a male rail moving 44.8 kilometers (27.8 miles) over 43 days (Casazza et al. 2008).

A 1991-1992 radiotelemetry study in south San Francisco Bay indicated an average home range of 4.7 hectares (11.6 acres) and an average core use area of 0.9 hectare (2.2 acres) (Albertson 1995).

The breeding period of the California clapper rail is prolonged. Pair bonding and nest building are generally initiated by mid-February. Nesting may begin as early as late February or early March (Evens and Page 1983) and extend through July in the south Bay, and into August in the north Bay (DeGroot 1927, U.S. Fish and Wildlife Service unpubl. Data in U.S. Fish and Wildlife Service 2013). There appears to be a break in nesting between mid-May through late June in the north Bay, a period that corresponds to the highest summer tides (Evens and Page 1983). Two peaks in nesting activity occur, a greater peak between mid-April and early May and a lesser peak between late June and early July (DeGroot 1927, Applegarth 1938, Gill 1972, Harvey 1988). The second nesting peak has been interpreted as attempts by late nesters (DeGroot 1927), second attempts after initial nesting failures (Gill 1972), or second broods (Wilbur and Tomlinson 1976).

The only estimates of annual adult California clapper rail survivorship are relatively low, ranging from 0.49 to 0.52 (Albertson 1995). These are similar to survival estimates reported for the Yuma subspecies (Eddleman 1989). Increased predation occurs during extreme winter high tides, probably due to increased movement of rails at this time when little cover is available (Albertson and Evens 2000). Adult survivorship has been suggested as the key demographic variable associated with survival of clapper rail populations (Foin et al. 1997).

Clapper rails are at least seasonally monogamous, and defend overlapping year-round territories (Zembal et al. 1989, Albertson 1995, Garcia 1995). Males perform most of the nest building (Meanley 1985). Rails frequently build several nest platforms, but use only one for incubation (Applegarth 1938, Gill 1972, Wilbur and Tomlinson 1976). Nests must be built at an elevation that protects the bowl from complete inundation during high tides (Evens and Collins 1992, Collins et al. 1994).

Egg-laying often begins prior to completion of the nest (Eddleman and Conway 1998). Both sexes share in incubation, which lasts from 18 to 29 days (Taylor 1996). Eggs are approximately 45 millimeters (1.77 inch) in length, and light tan or buff-colored with cinnamon-brown or dark lavender spotting concentrated at the broader end. Clutch size ranges from 5 to 14 eggs (DeGroot 1927, Gill 1972). Hatching is generally synchronous, but eggs may hatch one to several days apart (U.S. Fish and Wildlife Service 2013). After hatching, adults remain with the chicks for up to five to six weeks (Applegarth 1938, Meanley 1985).

Several studies from across the species’ range from 1988 through 1999 (Harvey 1988, Foerster et al. 1990, Schwarzbach et al. 2006) demonstrate nest success (the rate of nests having at least one egg hatch) of 32% to 56%, hatching success (the rate of eggs hatched per total eggs laid) of 19% to 41%, and a predation rate of 30% to 39%. Normal hatching success of other clapper rail eggs can be much higher (Kozicky and Schmidt 1949).