The present work aims at evaluating the ability of the River Tiber natural microbial community to degrade naproxen in water samples collected downstream from a wastewater treatment plant. For this purpose, different water microcosms were set up (microbiologically active vs sterile ones) and treated with naproxen (100 μg/L) alone or in the co-presence of gemfibrozil in order to evaluate if the co-presence of the latter had an influence on naproxen degradation. The experiment was performed in the autumn and was compared with the same experimental set performed in spring of the same year to highlight if seasonal differences in the river water influenced the naproxen degradation. Pharmaceutical concentrations and microbial analysis (total cell number, viability, and microbial community composition) were performed at different times in the degradation experiments. The overall results show that the natural microbial community in the river water had a key role in the naproxen degradation. In fact, although there was a transient negative effect on the natural microbial community in all the experiments (3 h after adding the pharmaceutical), the latter was able to degrade naproxen within about 40 days. On the contrary, no decrease in the pharmaceutical concentration was observed in the sterile river water. Moreover, the co-presence of the two drugs lengthened the naproxen lag phase. As regards the natural microbial community composition detected by Fluorescence in situ Hybridization, Alpha and Gamma-Proteobacteria increased when the pharmaceutical halved, suggesting their role in the degradation. This study shows that with the concentration studied, naproxen was degraded by the natural microbial populations collected from a river chronically contaminated by this pharmaceutical.