Nutrient transfers from the land to rivers have the potential to cause persistent eutrophic impacts at low flows even though the transfers may constitute a minor percentage of total annual fluxes. In rural catchments, the contribution from agricultural soils during storm events can be particularly large and untangling the relative contributions from multiple sources that vary in time and space is especially problematic. In this study, the potential for domestic septic tank system pollution during low flows was investigated in 3 small catchments (3 to 5 km(2)) Using an integrated series of methods. These included septic system surveys, continuous (10 min) total phosphorus (TP) monitoring at the outlet of each catchment, repeated low-flow water quality surveys in sub-catchments upstream of the catchment outlets and single day river-walk water quality surveys. A series of faecal matter and grey-water fingerprinting techniques were also employed. These included determining sterol ratios in stream sediments, monitoring the presence of proteins, E. coli and enterococci bacteria] signatures and boron. The total density and density of poorly maintained septic systems mirrored the magnitude of frequent TP concentrations in the catchments although this relationship was less apparent in the nested sub-catchments. The exception was possibly related to the simple hydraulics in one particular catchment and indicated temporary effluent attenuation in the other catchments. Repeated low-flow and river-walk water quality surveys highlighted discrete areas and reaches where stepped changes in nutrient concentration occurred. Bio-chemical fingerprinting showed that between 7% and 27% of sediments were contaminated with human faecal material and correlation matrices indicated that, at least during low flows, P fractions were positively correlated with some markers of faecal and grey-water contamination. (C) 2007 Elsevier B.V. All rights reserved.