Urban stormwater is regarded as a key input of faecal contamination in receiving water bodies and therefore, a major concern for health risks associated with aquatic recreation. Wastewater leakages, cross connections and overflows, together with faeces washed from surfaces during rainfall events, are possible origins of faecal contamination which enter these water bodies through stormwater drains. This paper applies conceptual models to a case study of the Yarra River estuary to understand the relative importance of fluxes derived from an urban creek and the 219 urban stormwater pipes which drain directly to the estuary as compared with other inputs, such as the Yarra River itself. Existing hydrologic-microorganism models were used for the estimation of the inputs from riverine and urban stormwater fluxes. These predictions were applied as boundary conditions for a new, highly simplified, model which accounts for the transport and survival of faecal microorganisms in the estuary. All models were calibrated using a rich dataset, containing over 2,000 measured Escherichia coli concentrations. Mass balances from the riverine and stormwater models indicate the limited influence of urban stormwater drains on the estuary during dry weather; less than 0.05% to 10% (5th and 95th percentile; median 0.5%) of the total daily E. coli load entering the estuary was derived from urban stormwater drains. While wet weather contributions from stormwater drains could be more significant (2% to 50%; 5th and 95th percentile), the average contribution remained marginal (median 10%). Sensitivity testing of the estuarine microorganism model by switching off stormwater boundary conditions resulted in minimal model efficiency reduction; this may reflect the low average daily contribution from urban stormwater drains. While these results confirm previous studies which show that E. coli loads derived from stormwater drains are dwarfed by other inputs, it is essential to note that these results also demonstrate that some conditions reveal the opposite; high proportions from stormwater are possible when combined with low riverine inputs and high urban rainfall. Furthermore, this study focuses on the overall impacts of direct urban stormwater inputs on the faecal contamination levels within the estuary, and localized impacts would certainly require further investigation.