Reliance on coliform monitoring of ground waters is slowly changing as is reflected in the proposed US EPA Ground Water Rule. In line with this we have investigated the use of an expanded range of faecal indicators and potential surrogate analytes within the Gwelup and Jandakot borefields in Perth, Western Australia. The aims of the study included comparing contamination in bores and surface waters in vulnerable locations, quantifying aquifer removal of microorganisms, trialing novel biochemical pollution indicators such as faecal sterols, assessing Escherichia coli as a measure of groundwater contamination and generating data for risk assessments. Sampling was undertaken of nine production bores, nine monitoring bores and four surface waters for 32 parameters comprising seven microbial indicators, 12 physico-chemical parameters and 13 biomarkers (including 8 faecal sterols and caffeine) at sampling stations potentially impacted by urban development. Concentrations of microbial indicators and biomarkers followed the pattern: basins >> monitoring bores >> production bores. Only one production bore sample contained bacterial indicators (0.1 enterococci.100 mL-1 on 1 occasion). Of the faecal biomarkers, coprostanol was generally at background levels. Cholesterol appeared to be a more sensitive measure of infiltration, but was also effectively removed. E. coli appeared to be a less sensitive indicator than enterococci. None of the physico-chemical parameters were useful surrogates. Overall apparent faecal microbial removal by aquifer filtration averaged >4-5 logs (not accounting for viruses). To maximise warning time and assay sensitivity it is suggested that enterococci be considered as the key bacterial indicator rather than E. coli and that different combinations of indicators and biomarkers be used to identify aquifer locations at risk, the presence of significant faecal material, and the likely presence of pathogens.