Aquatic ecosystems are being degraded by anthropogenic pollution on a global scale. Septic tank systems (STS), which are widely distributed in rural and peri-urban areas, are one potential source of water pollution. Although generally regarded as the most efficient method for on-site treatment of domestic wastewater, we question whether current regulation and management of these systems are sufficient to guarantee that they function effectively. Here, we present watershed-specific examples that illustrate some of the problems that arise when many years of inadequate regulation and management result in a legacy of failing STS that can become long-term, chronic sources of nutrient pollution. Our data suggest that more accurate accounting of the location, performance, and degree of failure of STS, and more research into their impacts on water quality, would improve sourceattribution of pollutants within rural watersheds. This would ensure that education of homeowners, mitigation, interdisciplinary research, and technological innovation could be targeted in a cost-effective way.