Sustaining natural levels of base flow is critical to maintaining ecological function as stream catchments are urbanized. Research shows a variable response of stream base flow to urbanization, with base flow or water tables rising in some locations, falling in others, or elsewhere remaining constant. The variable baseflow response is due to the array of natural (e.g., physiographic setting and climate) and anthropogenic (e.g., urban development and infrastructure) factors that influence hydrology. Perhaps as a consequence of this complexity, few simple tools exist to assist managers to predict baseflow change in their local urban area. This paper addresses this management need by presenting a decision support tool. The tool considers the natural vulnerability of the landscape, together with aspects of urban development in predicting the likelihood and direction of baseflow change. Where the tool identifies a likely increase or decrease it guides managers toward strategies that can reduce or increase groundwater recharge, respectively. Where the tool finds an equivocal result, it suggests a detailed water balance be performed. The decision support tool is embedded within an adaptive-management framework that encourages managers to define their ecological objectives, assess the vulnerability of their ecological objectives to changes in water table height, and monitor baseflow responses to urbanization. We trial our framework using two very different case studies: Perth, Western Australia, and Baltimore, Maryland, USA. Together, these studies show how pre-development water table height, climate and geology together with aspects of urban infrastructure (e.g., stormwater practices, leaky pipes) interact such that urbanization has overall led to rising base flow (Perth) and falling base flow (Baltimore). Greater consideration of subsurface components of the water cycle will help to protect and restore the ecology of urban freshwaters.