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Increasing residential development in watershed recharge areas increases the likelihood of groundwater and surface water contamination by wastewater effluent, particularly where on-site sewage treatment is employed. This effluent contains a range of compounds including those that have been demonstrated to mimic or interfere with the function of natural hormones in aquatic organisms and humans. To explore whether groundwater contaminated by discharge from on-site septic systems affects water quality in surface water ecosystems, we measured steroidal hormones, pharmaceuticals, and other organic wastewater compounds (OWCs) in water collected from six aquifer-fed ponds in areas of higher and lower residential density on Cape Cod (Massachusetts, USA). We detected both a greater number and higher concentrations of OWCs in samples collected from ponds located in higher residential density areas. Most often detected were the steroidal hormones androstenedione, estrone, and progesterone and the pharmaceuticals carbamazepine, pentoxifylline, sulfamethoxazole, and trimethoprim. Of particular concern, estrogenic hormones were present at concentrations approaching those that induce physiological responses in fish. While a number of papers have reported on surface water contamination by OWCs from wastewater treatment plants, our results show that surface water ecosystems in unconfined aquifer settings are susceptible to contamination by estrogenic and other biologically active OWCs through recharge from aquifers contaminated by residential septic systems.