A decline in the walleye Stizostedion vitreum sport fishery in lower Lake Oahe, South Dakota, was documented in the early 1980s and has been attributed to poor natural reproduction and/or recruitment. Contaminants were suspected of causing low natural reproduction/recruitment in lower Lake Oahe as well as low hatchability of eggs produced from broodstock walleyes taken from lower Lake Oahe. Concentrations of dissolved selenium in the Cheyenne River, which enters lower Lake Oahe, have increased considerably over the last 15 years. To determine whether selenium concentrations contributed to the reproduction problems in the lower Lake Oahe walleye population, adult walleye were collected during spawning operations in April 1994, 1995, and 1996 to obtain tissue samples. Muscle, liver, reproductive tissue, and unfertilized eggs were analyzed with a modified fluorometric method for determining selenium concentrations in plants. These tissues were also analyzed for mercury content using cold-vapor atomic absorption. No statistical differences (p < 0.05) in selenium or mercury concentrations among sites could be determined that would explain differential walleye egg hatchability. Correlation analysis determined significant inverse associations existed between the gonadal somatic index of male walleye and gonadal tissue selenium concentrations (r = -0.41, p = 0.0012). Both walleye sexes exhibited significant inverse associations between the hepatic somatic index (HSI) and liver selenium concentrations (males r = -0.33, p = 0.0095; and females r = -0.38, p = 0.0034). Positive relationships existed for female walleye selenium concentrations in the liver and the ovaries (r = 0.37, p = 0.003) and the liver and muscle tissue (r = 0.28, p = 0.027). Mercury concentrations in walleye ovaries were positively correlated with HSI (r = 0.30, p = 0.0012), length (r = 0.36, p = 0.0046), relative weight (r = 0.36, p = 0.0054), and muscle concentrations (r = 0.49, p = 0.0001). Mercury concentrations in male walleye muscle were correlated with age (r = 0.57, p = 0.0001), length (r = 0.79, p = 0.0001), and mercury concentrations in the testes (r = 0.43, p = 0.0006).