Human use of pharmaceuticals results in the excretion and disposal of compounds that become part of municipal and domestic waste streams. On-site waste water disposal and leaking city sewer systems can provide avenues for the migration of effluent to the underlying aquifers. This research assessed the occurrence and persistence of 22 target pharmaceuticals in septic tank effluent and two shallow, coarse-grained aquifers in western Montana. Twelve compounds (acetaminophen, caffeine, codeine, carbamazepine, cotinine, erythromycin-18, nicotine, paraxanthine, ranitidine, sulfamethoxazole, trimethoprim, and warfarin) were detected in a high school septic tank effluent. Three of the 12 compounds, carbamazepine, sulfamethoxazole, and nicotine, were detected in the underlying sand and gravel aquifer after effluent percolation through a 2.0-m thick sand vadose zone. Sampling of a second sand, gravel, and cobble dominated unconfined aquifer, partially overlain by septic systems and a city sewer system, revealed the presence of caffeine, carbamazepine, cotinine, nicotine, and trimethoprim. The presence of carbamazepine and sulfamethoxazole in these aquifers appears to correlate with local usage based on a reported monthly prescription volume. This work highlights the need for expanding geochemical investigations of sewage waste impacted ground water systems to include sampling for selected pharmaceuticals.