The Asian clam, Corbicula fluminea, commonly used in engineered wetlands receiving tailwater, affects nitrogen compound transformation in water. This study investigates how a commonly observed antibiotic in tailwater, norfloxacin, impact nitrogen compound transformation in tailwater containing C. fluminea. The clam was exposed to artificial tailwater with norfloxacin (0, 0.2, 20, and 2000 μg/L) for 15 days. Water properties, C. fluminea ecotoxicity responses, microorganism composition and nitrification- or denitrification-related enzyme activities were measured. Results revealed norfloxacin-induced increases and reductions in tailwater NH4+ and NO2− concentrations, respectively, along with antioxidant system inhibition, organ histopathological damage and disruption of water filtering and digestion system. Microorganism composition, especially biodiversity indices, varied with medium (clam organs and exposure water) and norfloxacin concentrations. Norfloxacin reduced NO2− content by lowering the ratio between microbial nitrifying enzyme (decreased hydroxylamine oxidoreductase and nitrite oxidoreductase activity) and denitrifying enzyme (increased nitrate reductase and nitrite reductase activity) in tailwater. Elevated NH4+ content resulted from upregulated ammonification and inhibited nitrification of microorganisms in tailwater, as well as increased ammonia emission from C. fluminea due to organ damage and metabolic disruption of the digestion system. Overall, this study offers insights into using benthic organisms to treat tailwater with antibiotic residues, especially regarding nitrogen treatment.