The Taunton River is the longest un-dammed coastal river in New England. With a watershed area encompassing approximately 562 square miles, it is the second largest watershed in Massachusetts. It is also one of the flattest, with only a twenty-foot elevation drop along its forty-mile main stem length. The basin contains 108 sub-watersheds and encompasses all or part of 43 municipalities. The water balance in a watershed describes the natural equilibrium of inputs and exports of water. Alterations to the natural water cycle occur primarily as a result of the human necessities of water supply withdrawals, wastewater discharges, and stormwater management that change the volumes and rates of water exchange between precipitation, surface water, groundwater and the atmosphere. A water budget tool was developed for this study to evaluate the hydrologic impacts associated with water supply withdrawals, wastewater discharges and stormwater runoff associated with land uses. The method uses a mass balance approach that accounts for net changes in groundwater recharge as it relates to base flow to streams and wetlands on an annual basis. It estimates stream base flow changes resulting from water withdrawal, water transfer, wastewater discharges and stormwater runoff associated with different land uses. The tool was originally developed as a spreadsheet pilot study, and then converted to a GIS-based script capable of automating the procedure for all 108 subwatersheds. The water balance tool revealed that many sub-watersheds in the upper Taunton Watershed are highly out of balance compared to natural conditions as a result of water transfers. The tool can also be used to evaluate alternative management scenarios such as changes in wastewater collection systems, water conservation measures to reduce water withdrawal volumes and improved stormwater management.