There is an ongoing need to monitor the status of imperiled fishes in the southeastern United States using effective methods. Visual surveys minimize harm to target species, but few studies have specifically examined their effectiveness compared to other methods or accounted for imperfect species detection. We used snorkel surveys to estimate detection probability and site occupancy for rare fishes in the Toccoa River system of north Georgia. We also carried out backpack electrofishing at a subset of sites to compare detection probabilities for both methods. The probability of detecting Percina aurantiaca (Tangerine Darter) and Etheostoma vulneratum (Wounded Darter) while snorkeling was relatively high, averaging 30% and 22%, respectively, and naïve and estimated occupancy rates (i.e., corrected for incomplete species detection) were almost identical for both species. The probability of detecting Erimystax insignis (Blotched Chub) while snorkeling was relatively low (9%), and their estimated occupancy rate (86%) was much higher than we detected in our survey. Detection was negatively related to depth and substrate size for Blotched Chub and positively related to depth for Tangerine Darter. Compared to snorkeling, the probability of detecting a species while backpack electrofishing was higher for Wounded Darter (40%) and comparable for Blotched Chub (11%). Tangerine Darter, however, were never captured while electrofishing even though they occurred at all four sites where both methods were used. Our study demonstrates the successful use of snorkel sampling to estimate occupancy rates of rare fishes in a large, clear southeastern river and illustrates the importance of accounting for imperfect species detection.