Understanding effects of human water use and subsequent return flows on the availability and suitability of water for downstream uses is critical to efficient and effective watershed management. We compared spatially detailed estimates of stream chemistry within three watersheds in diverse settings to available standards to isolate effects of wastewater and irrigation return flows on the suitability of downstream waters for maintaining healthy aquatic ecosystems and for selected human uses. Mean-annual flow-weighted total and source-specific concentrations of nitrogen and phosphorus in individual stream reaches within the Upper Colorado, Delaware, and Illinois River Basins and of total dissolved solids within stream reaches of the Upper Colorado River Basin were estimated from previously calibrated regional watershed models. Estimated concentrations of both nitrogen and phosphorus in most stream reaches in all three watersheds (at least 78%, by length) exceed recommended standards for the protection of aquatic ecosystems, although concentrations in relatively few streams exceed such standards due to contributions from wastewater return flows, alone. Consequently, efforts to reduce wastewater nutrient effluent may provide important local downstream benefits but would likely have minimal impact on regional ecological conditions. Similarly, estimated mean-annual flow-weighted total dissolved solids concentrations in the Upper Colorado River Basin exceed standards for agricultural water use and (or) the secondary maximum contaminant level (SMCL) for drinking water in 52% of streams (by length), but rarely due to effects of irrigation return flows, alone. Dissolved solids in most tributaries of the Upper Colorado River are attributable primarily to natural sources.