Urban beaches can be impacted by faecal pollution, but management actions to resolve the causes of contamination are often obfuscated by the inability of standard faecal bacteria analyses to discriminate sources of faecal material or detect microbiological hazards. We aimed to determine the causes, spatial extent, and point sources of faecal contamination within Rose Bay, a highly urbanised beach within Sydney, Australia's largest city, using molecular microbiological approaches. Sampling was performed across a network of transects originating from nine stormwater drains located on Rose Bay beach over the course of a significant rainfall event. 16S rRNA amplicon sequencing was also used to discriminate microbial signatures of faecal contamination. Using 16S amplicon sequencing, several 'indicator taxa' for stormwater contamination were identified and the Bayesian SourceTracker tool was used to model the relative impact of specific stormwater drains on the surrounding environment, revealing a heterogeneous contribution of discrete stormwater drains during different periods of the rainfall event.