This paper outlines the application of faecal source tracking (FST) tools in waterways in Southeast Queensland (SEQ), Australia. FST tools used in the case studies include biochemical fingerprinting, antibiotic resistance analysis, bacterial markers, viral markers and faecal sterols. These tools are predominantly used to identify sewage pollution in environmental waters sourced from defective septic systems or discharges from sewage treatment plants (STPs). The earlier case studies employ library-dependent FST tools where as the recent studies focus more on validation and application of library-independent tools. Several case studies reported the presence of sewage pollution in various aquatic environments and suggest that library-independent tools such as bacterial and viral markers are appealing because of the high specificity and sensitivity of these markers to differentiate and detect sewage and animal faecal pollution. A few case studies also used a combination of tools and suggested that such an approach can compensate uncertainty when one tool fails to produce satisfactory results. These case studies indicate that current FST tools can be successfully applied for faecal pollution tracking in environmental waters in SEQ. This is particularly important for water quality managers who are charged with protecting water quality.