Urban water systems consist of natural and engineered flows of water interacting in complex ways. System complexity can be understood via mass conservative models that account for the interrelationships among all major flows and storages. We have developed a generic urban water system model in the R package CityWaterBalance. CityWaterBalance provides a reproducible workflow for studying urban water systems by facilitating automated retrievals of open data and post-processing with open source R functions. It allows the user to 1) rapidly assemble a quantitative, comprehensive assessment of flows thorough an urban area, and 2) easily change the spatial and temporal boundaries of analysis. We use CityWaterBalance to evaluate the water system in the Chicago metropolitan area on a monthly basis for water years 2001-2010. Results are used to consider 1) impacts of management decisions aimed at reducing stormwater and combined sewer overflows and 2) the significance of future changes in precipitation.