In this study, the biodegradation of sulfamethoxazole (SMX) as affected by temperature, humic acid (HA) and SMX concentrations was investigated by HPLC–MS/MS analysis based on water–sediment batch experiments. The first order decay model (C=C0×exp (−kt)) was best fitted for SMX biodegradation. SMX degradation significantly increased with elevated temperature (degradation rate was 82.9% at 25°C vs. 40.5% at 4°C in sediment), HA contents (30mg/L of HA facilitated SMX degradation rate at 90.1% vs. 82.9% by 5mg/L of HA). However, SMX degradation is not readily dependent on its initial concentrations (1, 2, 20, 50 and 100mg/L), which suggests a co-metabolism mechanism may involove in SMX biodegradation. The prevalence of Bacillus firmus and Bacillus cereus among the strains isolated and identified on the basis of 16s rDNA gene sequence implicates their potential efficiency at degrading SMX. Only less than 1% of the SMX was transformed into its metabolite N4-acetyl-sulfamethoxazole, suggesting the need to pay more attention to the parent SMX. Overall, the ubiquitous occurrence of SMX underscores the need to explore better solutions for its removal and to mitigate this risk to public health.