The present study evaluated Se bioaccumulation in four waterbird species (n = 206 birds) that breed within San Francisco Bay, California, USA: American avocets (Recurvirostra americana), black-necked stilts (Himantopus mexicanus), Forster's terns (Sterna forsteri), and Caspian terns (Hydroprogne caspia). Selenium concentrations were variable and influenced by several factors, including species, region, reproductive stage, age, and sex. Adult Se concentrations (μg/g dry wt) in livers ranged from 3.07 to 48.70 in avocets (geometric mean ± standard error, 7.92 ± 0.64), 2.28 to 41.10 in stilts (5.29 ± 0.38), 3.73 to 14.50 in Forster's terns (7.13 ± 0.38), and 4.77 to 14.40 in Caspian terns (6.73 ± 0.78). Avocets had higher Se concentrations in the North Bay compared to the South Bay, whereas stilt Se concentrations were similar between these regions and Forster's terns had lower Se concentrations in the North Bay compared to the South Bay. Female avocets had higher Se concentrations than male avocets, but this was not the case for stilts and Forster's terns. Of the factors assessed, reproductive stage had the most consistent effect among species. Prebreeding birds tended to have higher liver Se concentrations than breeding birds, but this trend was statistically significant only for Forster's terns. Forster's tern chicks had lower Se concentrations than Forster's tern adults, whereas avocet and stilt adults and chicks were similar. Additionally, body condition was negatively related to liver Se concentrations in Forster's tern adults but not in avocet, stilt, or Caspian tern adults and chicks. These variable results illustrate the complexity of Se bioaccumulation and highlight the need to sample multiple species and examine several factors to assess the impact of Se on wildlife.