<p>Aquatic environments receive large amounts of effluents from sewage treatment plants (STPs). However, its quality does not always meet European standards, affecting other human activities, e.g., bathing during the summer season. We used the freshwater pearl mussel, <i>Margaritifera margaritifera</i>, to investigate the role of freshwater mussels in improving water quality after receiving effluents from STPs. First, we measured key water quality indicator parameters and assessed the freshwater mussel community. Second, through an <i>in situ</i> experiment, we assessed how mussels can reduce the pathogenic load to levels considered safe for human use during summer base flow conditions. Field surveys indicated that <i>Escherichia coli</i> levels surpassed those considered safe for bathing or consumption. At the experimental scale, however, mussels were able to reduce the pathogenic load to levels considered safe for bathing. These results highlight the importance of preserving freshwater biodiversity for improving environmental security.</p>