Urban water balances are generally unknown, yet they are necessary for assessing water availability in an urbanizing world and for understanding the effects of urbanization on the hydrologic cycle. We assess the spatial and temporal variability of water balances of 65 watersheds in the Baltimore, MD, metropolitan area during Water Years 2001–2009. Each water balance term is quantified independently and includes both natural (precipitation, evapotranspiration, streamflow) and piped (sewer infiltration and inflow [I&I], lawn irrigation, water supply pipe leakage) watershed inflows and outflows. The analysis also compares Gravity Recovery and Climate Experiment storage data with changes in storage calculated using the residual between watershed inflows and outflows. We find that when considering only natural water balance terms, the water balance residual (inflows minus outflows) increases with urbanization, largely as a result of the decrease in evapotranspiration as modeled by the land surface model Global Land Data Assimilation System/Noah. During wet years, the difference between urban and rural natural water balance residuals narrows because of increased urban streamflow. Excess water of the natural water balance in urban areas is largely exported by I&I into wastewater collection pipes; for some urban watersheds this excess is greater than gauged annual streamflow. I&I also outweighs piped inputs from lawn irrigation and water supply pipe leakage in the Baltimore area analysis. The net effect of piped flows on the urban water balance is a watershed export ranging between 300 and 465 mm/yr, underscoring the importance of interactions between engineered water and wastewater infrastructure and natural water balance components.