We examined factors influencing mercury concentrations in pre-breeding American avocets (Recurvirostra americana) and black-necked stilts (Himantopus mexicanus), the two most abundant breeding shorebirds in San Francisco Bay, California. We tested the effects of species, site, sex, year, and date on total mercury concentrations in blood of pre-breeding adult birds and used radio telemetry to determine space use and sites of dietary mercury exposure. We collected blood from 373 avocets and 157 stilts from February to April in 2005 and 2006, radio-marked and tracked 115 avocets and 94 stilts, and obtained 2393 avocet and 1928 stilt telemetry locations. Capture site was the most important factor influencing mercury concentrations in birds, followed by species and sex. Mercury concentrations were higher in stilts (geometric mean: 1.09 μg g^− 1 wet weight [ww]) than in avocets (0.25 μg g^− 1 ww) and males (stilts: 1.32 μg g^− 1 ww; avocets: 0.32 μg g^− 1 ww) had higher levels than females (stilts: 1.15 μg g^− 1 ww; avocets: 0.21 μg g^− 1 ww). Mercury concentrations were highest for both species at the southern end of San Francisco Bay, especially in salt pond A8 (stilts: 3.31 μg g^− 1 ww; avocets: 0.58 μg g^− 1 ww). Radio telemetry data showed that birds had strong fidelity to their capture site. Avocets primarily used salt ponds, tidal marshes, tidal flats, and managed marshes, whereas stilts mainly used salt ponds, managed marshes, and tidal marshes. Our results suggest that variation in blood mercury concentrations among sites was attributed to differences in foraging areas, and species differences in habitat use and foraging strategies may increase mercury exposure in stilts more than avocets.