Treated wastewater (effluent) has been used as a water source for aquifer recharge and sustaining perennial surface water flow. Artificial recharge basins allow effluent to seep into the ground relieving stressed aquifers. However, these basins frequently become clogged due to physical, chemical, and biological processes. Effluent is also used to replace baseflow for dry streambeds. However, little is known about the effect of effluent on stream-aquifer interactions. Effluent from the Nogales International Waste Water Treatment Plant sustains perennial flow in the Upper Santa Cruz River, Arizona. A series of monthly field campaigns were undertaken to understand the impact of effluent on the streambed at 16 different sites along a 30 km river reach. The field campaigns had two foci: physical transformations in the streambed and water source identification using chemical composition. Historic data sets including USGS stream gauging records, NIWTP outfall data, ADWR well transducer data and USGS well chemistry data were also analyzed to provide a larger context for the work. Results indicate that localized clogging forms in the Upper Santa Cruz River. The clogging layers perch the stream and shallow streambed causing a desaturation below the streambed. A clogging cycle is established in the context of a semi-arid hydrologic cycle: formation during dry and hot pre-monsoon months, and removal by a set of large flood flows (10+ m3/sec) during the monsoon season. However, if the intensity of flooding during the semi-arid hydrologic cycle is lessened, the dependent riparian area can experience a die off.