Spatial heterogeneity in the subsurface of karst environments is high, as evidenced by the multiphase porosity of carbonate rocks and complex landform features that result in marked variability of hydrological processes in space and time. This includes complex exchange of various flows (e.g., fast conduit flows and slow fracture flows) in different locations. Here, we integrate various “state-of-the-art” methods to understand the structure and function of this poorly constrained critical zone environment. Geophysical, hydrometric, and tracer tools are used to characterize the hydrological functions of the cockpit karst critical zone in the small catchment of Chenqi, Guizhou Province, China. Geophysical surveys, using electrical resistivity tomography (ERT), inferred the spatial heterogeneity of permeability in the epikarst and underlying aquifer. Water tables in depression wells in valley bottom areas, as well as discharge from springs on steeper hillslopes and at the catchment outlet, showed different hydrodynamic responses to storm event rainwater recharge and hillslope flows. Tracer studies using water temperatures and stable water isotopes (δD and δ18O) could be used alongside insights into aquifer permeability from ERT surveys to explain site- and depth-dependent variability in the groundwater response in terms of the degree to which “new” water from storm rainfall recharges and mixes with “old” pre-event water in karst aquifers. This integrated approach reveals spatial structure in the karst critical zone and provides a conceptual framework of hydrological functions across spatial and temporal scales.