Gillichthys mirabilis population static measurements (abundance, age, and size class structures) and vital rates (growth, mortality, recruitment) were monitored on an annual basis from 2002 to 2007. Population-level metrics were used to gauge habitat quality at two study sites (a contaminated site and a reference site) in two large northern California estuaries (San Francisco and Tomales Bays). San Francisco Bay populations exhibited slower growth and higher mortality rates and contained higher amounts of contaminants than Tomales Bay. Recruitment rates were highest at contaminated sites (Stege Marsh and Walker Creek) in 3 years out of 5 years, suggesting low adult survival. This study suggests that population-level effects on a residential fish may be attributed to estuarine contamination on the US Pacific coast.