Shallow reaches of southeastern rivers (“shoals”) harbor riverweed (Podostemum ceratophyllum), which provides important habitat for several imperiled fishes. Maintenance of shoal habitats is a management goal, yet the physical processes that form and maintain shoals are unknown. Based on field observations of variation in shoal characteristics, we identified two shoal types for which we hypothesized two different formation mechanisms: “alluvial” shoals formed by sediment inputs from tributaries, and “bedrock” shoals associated with bedrock sills. To test our hypothesis, we mapped shoal locations along 72km of the Etowah River (Georgia, U.S.A.), and estimated %gravel-cobble and %bedrock for each shoal. Results indicate that shoals with high %gravel-cobble (“alluvial” shoals) are commonly associated with tributary confluences, while shoals with high %bedrock showed no relationship to tributary confluences. Because alluvial shoals are wider than bedrock shoals and riverweed occurrence increases with channel width and sediment size, our continuing research will test the hypothesis that coarse-grained alluvial shoals have highest riverweed occurrence. Thus, tributary confluences may play an important role in maintaining imperiled fish populations in southeastern rivers, and management of coarse sediment transport in tributaries may be an especially important management focus for shoal-dependent imperiled fishes.