The influence of built urban infrastructure on stream chemistry was quantified throughout the drainage network of the tropical Río Piedras watershed, San Juan metropolitan area, Puerto Rico. Urbanization and failing domestic wastewater infrastructure appeared to drive changes in surface water chemistry throughout the watershed. Mean baseflow concentrations of chloride (Cl), ammonium (NH₄), dissolved organic carbon (DOC), dissolved organic nitrogen (DON), and phosphate (PO₄) all increased with urban infrastructure, while nitrate (NO₃) and dissolved oxygen (DO) decreased. These patterns in stream chemistry suggest that sewage effluent from failing or illegally connected sewer pipes has a major impact on surface water quality. Concentrations of Cl, DO, and NH₄ in stream water were most strongly related to sewer pipe volume, demonstrating the tight connection between urban infrastructure and stream chemistry. The loading and transformation of NO₃ and NH₄ were modeled along the river network and NH₄ loading rates from the landscape were strongly related to urban infrastructure, whereas NO₃ loading rates showed only weak relationships, highlighting the importance for incorporating NH₄ dynamics into river network models in urban environments. Water quality appears to be severely impacted by sewage in this tropical basin, despite large investments in built infrastructure. The high temperatures in the Río Piedras exacerbate water quality problems by reducing saturation DO levels in streams, and intense rainstorms tax the ability of built infrastructure to adequately manage overland flows. These problems are likely typical of much of the urbanized humid tropics.