Two of the main mechanisms of bacterial resistance to sulfonamides in aquatic systems, spread of antibiotic resistance genes (ARG) among the microbial community and in-situ bacterial sulfonamide degradation, were studied in mesocosms experiments using water and cobble biofilms from upstream (pristine waters) and downstream (polluted waters) from the Llobregat river, NE Iberian Peninsula. Mesocosms were prepared at two different concentrations (5000 ng/L and 1000 ng/L) of sulfonamides antibiotics (sulfamethazine and sulfamethoxazole). Concentrations of ARG, nutrients, sulfonamides and their degradation products were measured during the time course of the experiments. Sulfonamides were efficiently degraded by the biofilms during the first four weeks of the experiment. The abundance of ARG in biofilms sharply decreased after addition of high concentrations of sulfonamides, but this was not observed in the mesocosms treated with low concentrations of sulfonamides. Sulfonamide degradation was faster in polluted waters and at high concentrations of sulfonamide (and lower ARG abundances), suggesting that both degradation and ARG are two complementary resistance strategies employed by the microbial community. This study shows that microbial degradation of antibiotics is an efficient resistance mechanism coupled with the presence of ARG, and suggests that in situ degradation prevails at high concentrations of antibiotics whereas physiological adaptation by ARG spread would be more important under relatively lower concentrations of antibiotics.