Interest in understanding physical and hydraulic factors that might drive distribution and abundance of freshwater mussels has been increasing due to their decline throughout North America. We assessed whether the spatial distribution of unionid mussels could be predicted from physical and hydraulic variables in a reach of the Upper Mississippi River. Classification and regression tree (CART) models were constructed using mussel data compiled from various sources and explanatory variables derived from GIS coverages. Prediction success of CART models for presence-absence of mussels ranged from 71 to 76% across three gears (brail, sled-dredge, and dive-quadrat) and 51% of the deviance in abundance. Models were largely driven by shear stress and substrate stability variables, but interactions with simple physical variables, especially slope, were also important. Geospatial models, which were based on tree model results, predicted few mussels in poorly connected backwater areas (e.g., floodplain lakes) and the navigation channel, whereas main channel border areas with high geomorphic complexity (e.g., river bends, islands, side channel entrances) and small side channels were typically favorable to mussels. Moreover, bootstrap aggregation of discharge-specific regression tree models of dive-quadrat data indicated that variables measured at low discharge were about 25% more predictive (PMSE = 14.8) than variables measured at median discharge (PMSE = 20.4) with high discharge (PMSE = 17.1) variables intermediate. This result suggests that episodic events such as droughts and floods were important in structuring mussel distributions. Although the substantial mussel and ancillary data in our study reach is unusual, our approach to develop exploratory statistical and geospatial models should be useful even when data are more limited. ?? 2007 Springer Science+Business Media B.V.