This study explored the dynamic processes of algae-bacteria biofilms in the remediation of aquaculture pond effluents as a novel treatment strategy. The purification capacity of the biofilms, changes in community composition, and their impact on the dissemination of antibiotic resistance genes (ARGs) were investigated under the application of sulfamethoxazole (SMX) at concentrations ranging from 100 to 1000 μg/L. The study also considered the factors influencing the abundance and diversity of ARGs and mobile genetic elements (MGEs) across different seasons, including the roles of environmental parameters and microbial community structure.The results showed that, although exposure to SMX reduced nutrient removal efficiency, photosynthetic activity, and increased oxidative stress levels, the biofilms maintained relatively high purification efficiency (with nutrient removal rates ranging from 67.62 % to 93.23 % and SMX removal rate reaching 50.13 % ± 12.34 %), demonstrating adaptability to SMX stress. Network analysis identified key microbial carriers responsible for ARG dissemination, highlighting the complex interactions between environmental factors, microbial communities, and resistance gene propagation. These findings enhance our understanding of biofilm-based water treatment systems and the seasonal factors affecting the dynamics of ARGs and MGEs.