Groundwater-dependent ecosystems and species (GDEs) are found throughout watersheds at locations of groundwater discharge, yet not all GDEs are the same, nor are the groundwater systems supporting them. Groundwater moves along a variety of flow paths of different lengths and with different contributing areas, ranging from shorter local flow paths with low discharge and large seasonal variability to streams, springs and wetlands to longer regional flow paths with potentially larger discharge and low seasonal variability, commonly at low basin elevations. How does this variation in physical hydrology affect the type and distribution of GDEs? Using data on hypsographic position, groundwater-dependent species distributions, groundwater pumping and streamflow from Oregon, USA, we provide a conceptual model and initial supporting evidence demonstrating that spatial variation in groundwater flow path scales, illustrated using basin hypsography, is a driver of non-random distribution of GDEs across watersheds. Further, we posit that the spatial variation in primary stressors to groundwater (e.g. pumping and climate change) will differentially affect GDEs depending on their hypsographic position. Furthermore, because of their use for irrigation and municipal water supply, regional groundwater systems and associated species are more likely to be studied and receive regulatory protection. Our initial data point to a disproportionate focus on larger discharge, lower elevation GDEs, which leads to a bias in our understanding of the full suite of biodiversity associated with groundwater discharge as well as their stressors and potential mechanisms for protection.