Few studies have tested the influence of freshwater mussels on sediment properties and their potential influence on geomorphic processes outside of lab-based flume studies. Freshwater mussels have historically constituted a great proportion of the benthic biomass in many rivers in the southeastern United States and may maintain or transform the physical stability of river bed sediment indirectly by their biogenic structure or directly through processes including biodeposition and bioturbation. We tested the effects of freshwater mussels on sediment properties (D50 median grain size and sorting), sediment scour and reach scale bedload transport by deploying 36 mussel enclosures in the Sipsey River, Alabama, for a 9-week period. We employed a randomized design consisting of 4 replicates of the following treatments: 3 diversity treatments (Cyclonaias asperata; Fusconaia flava; Cyclonaias asperata and Fusconaia flava), 2 abundance treatments (24 indiv/m2, 48 indiv/m2), a sediment only control, and 2 sham mussel controls (24 indiv/m2, 48 indiv/m2). Sliding-bead monitors were installed in the center of each mussel enclosure to measure the amount of scour over the 9-week period, and biomodifications to surface layer D50 particle sizes and Folk and Ward sorting coefficients were measured using ImageJ photo analysis software. Hypothetical differences of bedload transport rates between reaches containing mussels (24 indiv/m2; 48 indiv/m2) and no mussels were computed using BAGS (Bedload Assessment in Gravel-bed Streams, Version 2008.11) bedload transport model. The results of this experiment suggest freshwater mussels contribute to bed scour, and increase surface layer D50 particle sizes and the degree of surface layer sorting. BAGS predicted that bedload transports rates in a reach with high abundances of freshwater mussels were lower than a reach containing no mussels (88.6% lower under baseflow conditions and 55.3% lower under bankfull flow conditions), based on biomodifications to surface layer D50 particle sizes and sorting by freshwater mussels. These results suggest that alterations to sediment properties by freshwater mussels are quantifiable in non-flume based settings, and that freshwater mussels may play a significant role as ecogeomorphic agents in the Sipsey River, AL, and other rivers that contain dense, long-lived communities of freshwater mussels.