River waters contain complex chemical mixtures derived from natural and anthropogenic sources. Aquatic organisms are exposed to the entire chemical composition of the water, resulting in potential effects at the organismal through ecosystem level. This study applied a holistic approach to assess landscape, hydrological, chemical, and biological variables. On-site mobile laboratory experiments were conducted to evaluate biological effects of exposure to chemical mixtures in the Shenandoah River Watershed. A suite of 534 inorganic and organic constituents were analyzed, of which 273 were detected. A watershed-scale accumulated wastewater model was developed to predict environmental concentrations of chemicals derived from wastewater treatment plants (WWTPs) to assess potential aquatic organism exposure for all stream reaches in the watershed. Measured and modeled concentrations generally were within a factor of 2. Ecotoxicological effects from exposure to individual components of the chemical mixture were evaluated using risk quotients (RQs) based on measured or predicted environmental concentrations and no effect concentrations or chronic toxicity threshold values. Seventy-two percent of the compounds had RQ values <0.1, indicating limited risk from individual chemicals. However, when individual RQs were aggregated into a risk index, most stream reaches receiving WWTP effluent posed potential risk to aquatic organisms from exposure to complex chemical mixtures.