Years of drought coupled with the expansion of urban centers in California have resulted in more municipalities relying on treated wastewater, or effluent, to recharge urban freshwater streams. Freshwater streams are important for nutrient cycling, sediment transport, habitat for native species, and other ecosystem functions. In urban environments, freshwater streams and their associated floodplains can be the only corridor that facilitates wildlife movement through a complex matrix of urban development. With changing climates, increases in population growth, and fluctuations in water demand, water management techniques such as effluent recycling have become a common strategy employed by municipalities to satisfy the multitude of water resource demands. Many wastewater treatment plants release a constant flow of effluent throughout the year, therefore removing the seasonal variability in which some floodplains may rely. As such, historically ephemeral streams within urban environments are transitioning towards perennial streams, modifying the configuration of floodplain habitats and potentially displacing species that rely on the non-aquatic components. Additionally, wastewater treatment plants alter the composition of constituents within the stream, a change that may have an effect on native species that rely on this resource. Through this lens we evaluate the impact of effluent on biodiversity within California, with a particular emphasis on federally and state-listed threatened and endangered species. We look at the effect various effluent-related constituents, such as salinity, has on the presence and distribution of native species that rely on freshwater habitats. We hypothesize that the increased salinity from wastewater treatment plants will have an adverse effect on aquatic species and also that a species' functional use of a floodplain system will dictate its response to an effluent-dominated stream. This response may vary depending on whether the associated species are aquatic, fossorial, or associated with riparian or aquatic vegetation. We compiled species occurrence data throughout the state from established repositories of species data. We organized this data according to watershed and according to proximity to established wastewater treatment plants. We mapped the co-occurrence of wastewater treatment plants and threatened and endangered species to determine the potential for changes in effluent management strategies to influence endangered species. The quantification of potential changes resulting from wastewater treatment plants is important for defining future management actions in relation to the preservation of floodplain terraces that act as terrestrial wildlife corridors, as well as to help prioritize land that needs to be maintained by a municipality or land that will potentially be entitled for development.