This results in high productivity since rails can nest again if the first nesting attempt fails. Nests are often built near sloughs or channels, in heavy marsh cover, and are often completely hidden from view by a canopy woven out of overhanging vegetation. A clutch may consist of six to nine pale eggs with rust colored spots. Both adults share in incubating the eggs. Although the inky black chicks can leave the nest almost immediately, care of the chicks may last for several weeks, as the adults protect the chicks and help them learn to forage.
Rails live in the marshes year round and appear to be relatively sedentary.
The nonbreeding season can be a very stressful time, because a series of extreme high tides flood the marshes each winter. Usually occurring three to four times monthly from October through February, these extreme tides cover most of the marsh vegetation, producing lake-like conditions. Rails are often left with little cover during these tides. The California clapper rail was once found in tidal salt marshes from Humboldt County to San Luis Obispo County. Historically, thousands of California clapper rails could be found in the marshes of San Francisco Bay.