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Abstract Geophysical methods have long been used in earth and environmental science for the characterization of subsurface properties. While imaging the subsurface opens the “black box” of subsurface heterogeneity, we argue here that these tools can be used in a more powerful way than characterization, which is to develop and test hypotheses. Critical zone science has opened new questions and hypotheses in the hydrologic sciences holistically around controls on water fluxes between surface, biological, and underground compartments. While groundwater flows can be monitored in boreholes, water fluxes from the atmosphere to the aquifer through the soil and the root system are more complex to study than boreholes can inform upon. Here, we focus on the successful application of various geophysical tools to explore hypotheses in critical zone hydrogeology and highlight areas where future contributions could be made. Specifically, we look at questions around subsurface structural controls on flow, the dimensionality and partitioning of those flows in the subsurface, plant water uptake, and how geophysics may be used to constrain reactive transport. We also outline areas of future research that may push the boundaries of how geophysical methods are used to quantify critical zone complexity. This article is categorized under:Water and Life > Nature of Freshwater EcosystemsScience of Water > Hydrological ProcessesWater and Life > Methods