Groundwater influenced ecosystems (GIEs) are increasingly vulnerable due to groundwater extraction, land use practices, and climate change. These ecosystems receive groundwater inflow, which can maintain water levels, water temperature, and chemistry necessary to sustain the biodiversity that they support. Many aquatic systems receive groundwater as a portion of their baseflow or water budget, and in some systems (e.g., springs, seeps, fens) this connection with groundwater is central to the system’s integrity and persistence. Groundwater management decisions for human use often do not consider the ecological effects of those actions on GIEs. This disparity can be attributed, in part, to a lack of information regarding the physical relationships these systems have with the surrounding landscape and climate, which may influence the environmental conditions and associated biodiversity. We estimate the vulnerability of GIEs in the Atlantic Highlands and Mixed Wood Plains EPA Level II Ecoregions in the northeastern United States. We represent vulnerability with variables describing adaptive capacity (topographic wetness index, hydric soil, physiographic diversity), exposure (climatic niche), and sensitivity (aquatic barriers, developed or agriculture areas).