The complex infrastructure and concentrated humasn activities in urban areas greatly affect the distribution of both water and elements in and around urban aquatic environments. Unlike more “natural” systems, the ecological, hydrological, and geochemical footprints of cities are much greater than the area of the city itself. In addition, cities themselves are diverse – a city's age, size, climate, building materials, stage of economic development, legacy of previous land uses, and environmental best management practices all exert influence over water quantity and quality. Within any individual urban area, land use and infrastructure age are heterogeneous, and pollution in the aquatic environment can occur both from point‐sources (e.g., wastewater effluent, construction, spills, long‐term leakage) and nonpoint sources (e.g., stormwater runoff). All of these factors combine to alter hydrologic systems and enhance chemical fluxes in urban areas. Only recently have urban systems become the focus of their own, unified approach to investigation within the environmental sciences. In this article, we discuss some of the issues that confound the understanding of the geochemistry of urban aquatic systems, including the impact of impervious surfaces, the effects of heterogeneity of land cover on water quality, and how urban areas function as “global” water polluters.