Overall fish abundance, abundance of introduced, native, and seasonal fish groups, and species diversity declined over a 14‐year period in Suisun Marsh, a portion of the San Francisco Bay estuary, and were associated with decreases in freshwater outflow and increases in salinity. Fish groups showed different patterns of abundance; large fluctuations in introduced and seasonal fish groups contrasted with a steady decline in native fish. Native species were found more often in small, dead‐end sloughs, seasonal species were found in larger sloughs, and introduced species were found in both habitats. Fish assemblage structure was less predictable than in an earlier (and shorter) study of the same community. Mixed groups of native and introduced species with similar freshwater and seasonal needs reflected effects of drought and increasing water diversions from the estuary. Chameleon goby Tridentiger trigonocephalus and yellowfin goby Acanthogobius flavimanus, two introduced species, fluctuated greatly in abundance in recent years, whereas other species declined steadily. Changes in fish abundance in the marsh reflect estuary‐wide changes and suggest that environmental disturbances coupled with introduced species are altering fish communities and hastening native fish declines.