The microbial contamination of urban stormwater has an important impact on human health and stormwater reuse. This study develops an exploratory semi-distributed model, MOPUS_S, which can simulate faecal coliform levels in separate sewer systems in urban catchments. The MOPUS_S was built by coupling the SWMM model and the microbial MOPUS model. The parameters associated with the deposition and wash-off of microorganisms were more influential than those related to microorganism survival processes. Compared to other existing bacterial models, MOPUS_S showed comparable performance in predicting faecal coliform concentrations. The performance varied largely between rainfall events, with Nash-Sutcliffe efficiency (NSE) values ranging from −5.03 to 0.39 and R 2 ranging from −0.02 to 0.83, respectively. The model simulation results for low and medium concentrations were better than those for the peak concentrations. Poor simulation results of peak concentrations obviously affect the overall model performance. In general, MOPUS_S could be capable of predicting the faecal coliform load in urban catchments and be a useful tool for urban stormwater management planning.