Cities are a confluence for environmental and man-made flows of water. Water supply, wastewater discharge, flooding and combined sewer overflow are some of the major, interdependent issues that cities seek to manage. Successful management depends on a quantitative understanding of the relationships among urban water flows and storages that is difficult to obtain. We have developed a reproducible workflow for evaluating the urban water system as the package CityWaterBalance for R. R is an open source language with many active users. CityWaterBalance builds upon existing R packages and open data to largely automate the process of evaluating the urban water network, including flows lacking data. It allows the user to 1) quickly assemble a quantitative, unified picture of flows thorough an urban area, and 2) easily change the spatial and temporal boundaries of analysis to match scales relevant to local decision-making. We used CityWaterBalance to evaluate the water system in the Chicago metropolitan area on a monthly basis for water years 2001-2010. Our analysis was used to consider 1) trade-offs associated with management alternatives for stormwater and combined sewer overflows and 2) the significance of future changes in precipitation. Our approach may be used as a scoping tool for considering interventions in the urban water system or to generate input datasets for more detailed studies.