Commercial salt evaporation ponds comprise a large proportion of baylands adjacent to the San Francisco Bay, a highly urbanized estuary. In the past two centuries, more than 79% of the historic tidal wetlands in this estuary have been lost. Resource management agencies have acquired more than 10 000 ha of commercial salt ponds with plans to undertake one of the largest wetland restoration projects in North America. However, these plans have created debate about the ecological importance of salt ponds for migratory bird communities in western North America. Salt ponds are unique mesohaline (5–18 g l⁻¹) to hyperhaline (> 40 g l⁻¹) wetlands, but little is known of their ecological structure or value. Thus, we studied decommissioned salt ponds in the North Bay of the San Francisco Bay estuary from January 1999 through November 2001. We measured water quality parameters (salinity, DO, pH, temperature), nutrient concentrations, primary productivity, zooplankton, macroinvertebrates, fish, and birds across a range of salinities from 24 to 264 g l⁻¹. Our studies documented how unique limnological characteristics of salt ponds were related to nutrient levels, primary productivity rates, invertebrate biomass and taxa richness, prey fish, and avian predator numbers. Salt ponds were shown to have unique trophic and physical attributes that supported large numbers of migratory birds. Therefore, managers should carefully weigh the benefits of increasing habitat for native tidal marsh species with the costs of losing these unique hypersaline systems.