The occurrence and estimated concentration of twenty illicit and therapeutic pharmaceuticals and metabolites in surface waters influenced by wastewater treatment plant (WWTP) discharge and in wastewater effluents in Nebraska were determined using Polar Organic Chemical Integrative Samplers (POCIS). Samplers were installed in rivers upstream and downstream of treated WWTP discharge at four sites and in a discharge canal at a fifth location. Based on differences in estimated concentrations determined from pharmaceuticals recovered from POCIS, WWTP effluent was found to be a significant source of pharmaceutical loading to the receiving waters. Effluents from WWTPs with trickling filters or trickling filters in parallel with activated sludge resulted in the highest observed in-stream pharmaceutical concentrations. Azithromycin, caffeine, 1,7-dimethylzanthine, carbamazepine, cotinine, DEET, diphenhydramine, and sulfamethazine were detected at all locations. Methamphetamine, an illicit pharmaceutical, was detected at all but one of the sampling locations, representing only the second report of methamphetamine detected in WWTP effluent and in streams impacted by WWTP effluent.