AimsTo determine the impact of septic systems on water quality and in so doing identify watershed level characteristics that influence septic system impact. Methods and ResultsWater samples were collected from streams in 24 well-characterized watersheds during baseflow to analyse for the levels of faecal indicators Escherichia coli and enterococci. The watersheds represent a gradient of land-use conditions from low to high density of septic systems, as well as developed to undeveloped uses. Our findings indicate statistically significant interaction between septic density and season for enterococci count (P=0005) and stream yield (P=004). Seasonal variations in bacterial count and stream yield were also observed, with significant differences between spring-winter and summer-winter. Results from multiple linear regression models suggest that watershed characteristics (septic system density, median distance of septic systems to stream, per cent developed area and forest cover) and water temperature could explain approximately half (R-2=050) of the variability in bacterial count and yield in spring and summer. ConclusionsThere is a significant positive relationship between septic system density and faecal pollution levels. However, this relationship is season dependent and is influenced by watershed level characteristics such as median distance of septic systems from streams, per cent developed area and forest cover. Significance and Impact of the StudyThis study confirms the significant impact of septic systems on faecal pollution during baseflow and provides the tools that will enable effective pollution monitoring at the watershed scale.