Pteronotropis welaka (Bluenose Shiner) has a fragmented range throughout the Southeast, but its apparent rarity may reflect a low probability of detection during surveys. Our objectives were to obtain up-to-date status information for populations in southwest Georgia and to account for incomplete detection in our estimate of the proportion of sites occupied. We detected Bluenose Shiner at 5 of 39 sites (13%) sampled during 2004 and 2005 and estimated detection probability (p) and the proportion of sites occupied (psi) from seine-haul data. Models containing habitat covariates as predictors of p and psi provided a better description of the data than models without covariates for Bluenose Shiner and three other minnow species. Regardless of the model structure, the probability of detecting Bluenose Shiner during a single seine haul was substantially lower than for the other minnow species (3–8% vs. 13–33%). However, estimates of the proportion of sites occupied (corrected for incomplete detection) were similar to observed occupancy rates for all four species because of the large number of seine hauls we made at each site. The modeling approach we followed increased our confidence in survey results and provided information on where and how much to sample in future surveys. It has broad application to future surveys and monitoring programs for rare aquatic species in the southeastern United States.