Widespread human water extractions and diversions have led managers to implement novel water conservation strategies, including the reuse of treated municipal wastewater. Wastewater treatment plants were born out of the need to protect water quality and prevent sewage from contaminating waterways. However, this resource has been utilized for numerous human (e.g., irrigation, drinking water, groundwater recharge) and conservation (e.g., stream and river recharge) needs in water scarce regions. To better understand the role treated municipal wastewater might play in helping society meet 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. One-third of the 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 these two resources—T&E species and effluent—are ultimately interconnected in ways that are important for water policy, suggesting that species conservation goals should be considered when making decisions about effluent allocations and reuse.