Septic tank systems (STS) are widely used to treat domestic wastewater from individual dwellings in rural areas but are a potential source of water pollution. However, their contribution to freshwater eutrophication and impacts on human health are uncertain and difficult to quantify. Five case studies are presented to highlight the issues underpinning this problem. Uncertainty exists over the numbers and locations of STS because registration is not fully implemented in all regions. Underestimating the numbers of STS located in a catchment can lead to overestimation of the relative contribution from diffuse sources such as agriculture. In turn, this may lead to potential delays in meeting water quality limits due to disproportionate targeting of potential sources. System performance is uncertain due to a lack of information on factors (such as siting, design, age, nature and level of maintenance, proximity to a watercourse) that affect nutrient retention rates. Many systems still discharge directly to a watercourse, or to a drainage network closely connected to a watercourse despite prohibition of such discharges. Their effect on water quality is also uncertain because current nutrient abatement policies ignore the temporal variation in nutrient loading that can influence ecological response in streams and connecting ditches. These case studies show that although STS constitute a relatively small (often <10%) portion of total annual catchment nutrient loads, they can still significantly increase in-stream nutrient concentrations, especially during low flow periods in summer. STS may therefore be a greater risk to riverine eutrophication and human health than is currently assumed. More sophisticated resolution of source apportionment is needed to fully capture water quality impairment due to clustering of STS along stream networks. Targeted surveys and public awareness campaigns are useful tools for identifying failing STS, improving STS maintenance and highlighting alternative treatment options for use in catchment areas that are especially sensitive or valuable. These case studies support the need for a risk-based policy of STS registration and regulation governing maintenance to avoid further declines in the ecosystem services our freshwaters provide.