Ecological constraints in subsurface environments relate directly to groundwater flow, hydraulic conductivitiy, interstitial biogeochemistry, pore size, and hydrological linkages to adjacent aquifers and surface ecosystems. Groundwater ecology has evolved from a science describing the unique subterranean biota to its current form emphasising multidisciplinary studies that integrate hydrogeology and ecology. This multidisciplinary approach seeks to elucidate the function of groundwater ecosystems and their roles in maintaining subterranean and surface water quality. In aquifer-surface water ecotones, geochemical gradients and microbial biofilms mediate transformations of water chemistry. Subsurface fauna (stygofauna) graze biofilms, alter interstitial pore size through their movement, and physically transport material through the groundwater environment. Further, changes in their populations provide signals of declining water quality. Better integrating groundwater ecology, biogeochemistry, and hydrogeology will significantly advance our understanding of subterranean ecosystems, especially in terms of bioremediation of contaminated groundwaters, maintenance or improvement of surface water quality in groundwater-dependent ecosystems, and improved protection of groundwater habitats during the extraction of natural resources. Overall, this will lead to a better understanding of the implications of groundwater hydrology and aquifer geology to distributions of subsurface fauna and microbiota, ecological processes such as carbon cycling, and sustainable groundwater management