The Santa Cruz River, in southern Arizona, receives steady inputs of nutrient-enriched treated wastewater (effluent). Previous studies have documented reduced infiltration of surface water in the river. This disruption of hydrologic connectivity, or clogging, can have consequences for groundwater recharge, flows of wastewater in unwanted locations, and potentially even survivorship of floodplain riparian vegetation. Clogging can result from biotic processes (microbial or algal growth), abiotic processes (siltation of interstitial spaces), or both. Little is known about clogging in rivers and the environmental factors that regulate their dynamics, so natural field experiments along the Santa Cruz and San Pedro Rivers were used to answer: 1) Are there spatial patterns of hydraulic conductivity in the riverbed downstream from the effluent point-source? 2) Is there temporal variability in hydraulic conductivity and microbial abundance associated with flooding? 3) Are there environmental variables, such as nutrients or stream flow, related to differences in hydraulic conductivity and microbial abundance? To address these questions, a series of sites at increasing distance from two municipal effluent discharge points with differing water quality were selected on the Santa Cruz River and compared with non-effluent control reaches of the San Pedro River. Physical, chemical, and biological parameters were monitored over one year to capture seasonal changes and flood cycles.