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Urbanization alters watershed ecosystem functioning, including nutrient budgets and processes of nutrient retention. It is unknown, however, how variation in stormwater infrastructure design affects the delivery of water and materials from urban watersheds. In this study, we asked: (1) How does stormwater infrastructure design vary over time and space in an arid city (Phoenix, Arizona, USA)?, and (2) How does variation in infrastructure design affect fluxes of dissolved nitrogen (N), phosphorus (P), and organic carbon (DOC) from urban watershed ecosystems? From 1955 to 2010, stormwater infrastructure designs shifted from pipes, to engineered channels and retention basins, to natural washes. We monitored 10 nested watersheds, where small (5-141 ha) watersheds had medium-density residential land use but differed in stormwater infrastructure, whereas larger watersheds (1,662-20,247 ha) had a variety of land uses and infrastructures. We measured rainfall in each watershed and discharge and dissolved N, P, and DOC concentrations in flow at each watershed outlet for runoff-generating rainfall events between 2010 and 2012. We used path analysis to test hypotheses about the relationships among infrastructure characteristics, land cover, storm characteristics (including antecedent conditions), and nutrient and DOC loads. We found that retention-basin density decreased and imperviousness increased runoff, which in turn increased nutrient and DOC delivery. Concentrations varied with antecedent conditions and rainfall but did not vary with watershed characteristics. We show that stormwater infrastructure creates heterogeneity in the hydrologic and biogeochemical function of urban watersheds and that stormwater management may represent a major source of ecosystem heterogeneity within and across cities.