Urbanization often alters the physical, chemical, and biological structure of aquatic ecosystems embedded within them, creating managed ecosystems with different structure and functioning as compared to their unmanaged counterparts. Our work focused on patterns in dissolved organic carbon (DOC) along a managed stream in Phoenix, Arizona. We documented longitudinal changes in DOC concentrations and quality (defined as chemical complexity and measured as specific ultraviolet absorbance at 254 nm, SUVA) along a 66 km stream dominated by treated wastewater effluent. DOC concentrations along the stream declined by an average of 64%, and chemical complexity increased substantially. We posed four hypotheses to explain changes in downstream water chemistry; including hydrologic dilution, microbial mineralization, abiotic sorption to suspended sediments, and photodegradation by ultraviolet (UV) radiation. Only the second and fourth hypotheses represent permanent removal mechanisms. Our data most strongly supported predictions from the dilution hypothesis and microbial mineralization as an explanation for the changes in DOC chemistry. Surface-subsurface water linkages were important but altered from unmanaged streams, as deep groundwater was used to augment surface flows. Variation in the use of groundwater was linked to human decision making and engineering related to water management. Reduction in geomorphic complexity increased the importance of dilution in explaining patterns but also increased the importance of UV oxidation as a mechanism influencing DOC chemistry. Our findings suggest urban stream management has shifted dependence on microbially mediated C removal mechanisms to hydrologic dilution to reduce output concentrations. This shift lowers contaminant removal potential and increases dependence on limited groundwater resources.