Self-purification is a key ecosystem service provided by riverine biota that is particularly important in polluted water bodies serving multiple societal uses, but the extent to which self-purification may be influenced by human uses is unknown. We studied a eutrophic lowland river used for drinking water and recreation to identify the maximal sustainable extent of human use. We recorded filtration by mussels and modeled the disturbance to mussels caused by wave action induced from recreational boating. Filtration was significantly affected by shear stress produced from boats down to a depth of 2.7 m. Threshold values for the intensity of wave disturbance ranged from 0.21 N/m² (Unio tumidus) to 0.43 N/m² (Anodonta anatina) for moderate effects and from 0.02 N/m² (U. tumidus) to 0.13 N/m² (Dreissena polymorpha) for no effects on filtration. Anodonta anatina and D. polymorpha showed a significantly lower degree of shell closing and a higher predicted medium-effect shear stress (the shear stress associated with 50% of the maximum shell closing duration) than U. tumidus and Unio pictorum, which probably results from differences in the species position in and above the sediment. Coupled hydraulic–ecological modeling showed that typical boating activity may reduce self-purification activity by mussels, with the extent of disturbance depending on mussel species, river depth, boating frequency, and cruising speed. Single passages of boats reduced daily mussel filtration rates by 0.02% for muscle-driven boats, 0.45% for yachts, 0.68% for motor boats, and 0.69% for motorized rafting and rowing boats. Depending on total daily boat traffic and hydrological conditions, a reduction in the daily filtration rate by mussel populations within the studied river section was estimated at 6.9%. We conclude that self-purification activity of this lowland river section is not significantly affected by recreational boating, but might be affected by more intense recreational boating under altered river flow conditions.