To reduce pesticide pollution and promote sustainable agricultural development in China, we designed a pilot-scale biofilter system to treat residual imidacloprid wastewater in an orchard. The biofilter system demonstrated a high rate of removal of imidacloprid from the biodegradation wastewater, with removal rates from the outlet exceeding 99% at different concentrations of pesticides. Among environmental factors, imidacloprid concentration at the inlet and biomixture significantly affected the activity of imidacloprid-degrading bacteria. The dominant microbial communities during the stable operation of the biofilter system included Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes at the phylum level and Bacillus, Methylobacter, and unclassified_f__Microbacteriaceae at the genus level. In future initiatives to improve biofilter performance and applicability, increasing attention should be paid to the dominant microbial communities, the number of biofilter units, and important environmental factors. Orchard workers in China should improve the existing treatment of residual pesticide wastewater to mitigate agricultural non-point source pollution.