A field study was conducted to investigate sewage inputs at popular anchorages in Moreton Bay, a sub-tropical, semi-enclosed embayment system in Southeast Queensland, Australia. Sterol biomarkers were quantified in sediments revealing low levels over a spatial and temporal scale consistent with a shallow, oligotrophic, highly dynamic, sand dominated system. Despite low concentrations (ng/g) and high variability, relevant sterol/stanol pairs remained well-correlated and were successful in identifying an unexpected once-off pollution event from a point source at Moreton Bay Island. During this incident, the main human sewage biomarker, coprostanol, was found at a concentration of 1.4 姯g, with a coprostanol/5a-cholestanol ratio of 3.2. Other than this one incident, sterol levels were consistently low even when anchorages were at full capacity. Thus, sewage from recreational vessels was found to have very little effect on sediment quality at anchorages in Moreton Bay and Gold Coast Broadwater.