Previous attempts to predict the importance of abiotic and biotic factors to unionids in large rivers have been largely unsuccessful. Many simple physical habitat descriptors (e.g., current velocity, substrate particle size, and water depth) have limited ability to predict unionid density. However, more recent studies have found that complex hydraulic variables (e.g., shear velocity, boundary shear stress, and Reynolds number) may be more useful predictors of unionid density. We performed a retrospective analysis with unionid density, current velocity, and substrate particle size data from 1987 to 1988 in a 6-km reach of the Upper Mississippi River near Prairie du Chien, Wisconsin. We used these data to model simple and complex hydraulic variables under low and high flow conditions. We then used classification and regression tree analysis to examine the relationships between hydraulic variables and unionid density. We found that boundary Reynolds number, Froude number, boundary shear stress, and grain size were the best predictors of density. Models with complex hydraulic variables were a substantial improvement over previously published discriminant models and correctly classified 65-88% of the observations for the total mussel fauna and six species. These data suggest that unionid beds may be constrained by threshold limits at both ends of the flow regime. Under low flow, mussels may require a minimum hydraulic variable (Rez.ast;, Fr) to transport nutrients, oxygen, and waste products. Under high flow, areas with relatively low boundary shear stress may provide a hydraulic refuge for mussels. Data on hydraulic preferences and identification of other conditions that constitute unionid habitat are needed to help restore and enhance habitats for unionids in rivers. ?? 2008 Springer Science+Business Media B.V.