Sustainable groundwater management provides an opportunity for environmental water needs to be considered and secured by establishing appropriate groundwater thresholds. Ecosystems that require access to groundwater for some or all their water requirements are referred to as groundwater dependent ecosystems (GDEs). However, large data gaps often exist around the cause-and-effect relationships between groundwater conditions and the impacts they have on GDEs. These data gaps are largely attributed to a lack of shallow monitoring wells near GDEs, and a lack of practical biological metrics to characterize ecosystem health. This transdisciplinary study explores the use of geophysics (electrical resistivity tomography) to fill in our understanding of shallow subsurface soil-hydrological conditions within GDEs. In addition, we develop an approach to characterize ecosystem health within GDEs, using groundwater-dependent vegetation (phreatophytes) as indicators. Ten vegetation variables were used to characterize six biological indicators—growth, diversity, recruitment, structure, native plant dominance, and survivorship—which were used to infer ecosystem health conditions. Health indicators for groundwater-dependent vegetation were found to directly correlate with subsurface conditions, where greater groundwater availability (higher soil moisture content and shallower groundwater levels) was associated with “healthier” vegetation. This study provides a new approach to integrate hydrological, geophysical, and biological data to strengthen monitoring programs and inform water resource management decisions.