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Abstract A changing climate and often unregulated water extractions have exposed over 2 billion people to water stress worldwide. While water managers have explored a portfolio of options to reduce this stress, supply augmentation through reuse of treated municipal wastewater is becoming increasingly attractive. Wastewater treatment plants protect water quality and prevent sewage from contaminating waterways. Increasingly, this resource is utilized for numerous human (e.g., irrigation, drinking water, groundwater recharge) and conservation (e.g., stream and river recharge) needs in water stressed regions. To understand the role treated municipal wastewater plays in impacting conservation objectives we identified the intersection of wastewater treatment plant locations and occurrences of threatened and endangered (T&E) species in California and compared the permitted contribution of effluent to baseflow quantities of the receiving waterbody to assess the degree to which changes in effluent could affect instream waterbodies. We found a positive correlation between the presence of treatment plants and T&E species in California watersheds—a quarter of species have 100% of their range in watersheds with at least one treatment plant. This correlation is greatest for species associated with terraces and riparian habitat, followed by aquatic habitat and aquatic emergent vegetation. One‐third of watersheds in our analysis can receive most of their cumulative watershed baseflow from effluent and are characterized by dense urbanization or agriculture. Our analysis demonstrates that the fates of T&E species and effluent are interconnected in ways important for water policy, suggesting that species conservation goals should be considered when making decisions about effluent reuse.