Summary Managers in the Upper Mississippi River (UMR) are using reductions in the River's water levels during summer to mimic historical water regimes and rehabilitate habitats for vegetation and other species. Concerns for the unintended effects of these actions on mussel populations threatened to halt these projects. Our objective was to characterise the survival and movement of two mussel species in the UMR associated with a water level drawdown. During 2009 (no drawdown) and 2010 (0.3 m summer drawdown), we glued passive integrated transponder tags to 10 Amblema plicata and 10 Lampsilis cardium at each of 11 sites. Five sites were in shallow areas expected to be minimally affected by the drawdown (reference sites), and six sites were in shallow areas expected to be directly affected by the drawdown (treatment sites). About equal numbers of sites within both the reference and treatment areas had low and high slopes. Tagged mussels were randomly allocated across sites (within years). Recovery of tagged mussels was >88% in 2009 and 2010. Mortality was similar and low (mean, c. 5% in both species) among reference sites but was variable and relatively high (means, c. 27% in L. cardium and c. 52% in A. plicata) among treatment sites; variation in mortality among treatment sites appeared related to slope. The study found evidence of drawdown associations with net horizontal movements in A. plicata but not L. cardium. Weekly horizontal movements in both species were significantly correlated with changes in water elevation. We observed significant slope associations related to the drawdown for mortality and net horizontal movement in A. plicata. There were strong species‐specific differences in the effects of the drawdown on mortality, vertical movement and horizontal movement. These results suggest that A. plicata responded to the drawdown by vertical movement into the substratum, whereas L. cardium responded by horizontal movement to deeper water. No directionality of movement was observed in either species. Collectively, these data suggest that drawdowns can influence the mortality, movement and behaviour of mussels in the UMR. However, more information on spatial and temporal distributions of mussels is needed to better understand the magnitude of these effects. Results from this study are being used by resource managers to better evaluate the effects of this management tool on native mussel assemblages.