Adult male greater scaup (Aythya marila) (GS), surf scoters (Melanitta perspicillata)(SS), and ruddy ducks (Oxyura jamaicensis) (RD) were collected from Suisun Bay and coastal Tomales Bay in the greater San Francisco Bay area to assess exposure to inorganic contaminants. Hepatic selenium (Se) concentrations were highest in GS (geometric mean = 67 ppm, dw) and SS (119 ppm) in Suisun Bay, whereas hepatic mercury (Hg) was highest (19 ppm) in GS and SS from Tomales Bay. Hepatic Se and Hg were lower in RD and did not differ between locations. Hepatic supernatants were assayed for enzymes related to glutathione metabolism and antioxidant activity including: glucose-6-phosphate dehydrogenase (G-6-PDH), glutathione peroxidase (GSH-peroxidase), glutathione reductase (GSSG-reductase), and glutathione-S-transferase (GSH-transferase). GSH-peroxidase activity was higher in SS and RD, and G-6-PDH higher in GS and SS from Suisun Bay than Tomales Bay. GSSG-reductase was higher in SS from Suisun Bay. The ratio of oxidized glutathione (GSSG) to reduced glutathione (GSH) was greater in all species from Tomales Bay. The following significant relationships were found in one or more species with increasing hepatic Hg concentration: lower body, liver and heart weights; decreased hepatic GSH concentration, G-6-PDH and GSH-peroxidase activities; increased ratio of GSSG to GSH, and increased GSSG-reductase activity. With increasing hepatic Se concentration, GSH-peroxidase increased but GSH decreased. It is concluded that measurement of associated enzymes in conjunction with thiol status may be a useful bioindicator to discriminate between Hg and Se effects. Concentrations of mercury and selenium and variable affected have been associated with adverse effects on reproduction and neurological function in experimental studies with mallards.