Groundwater-dependent ecosystems (GDEs) in arid and semiarid environments play significant ecological roles, and, yet in many parts of the world, these ecosystems have been drained for agricultural use. In wetlands containing acid sulfate soils, the altered hydrology may trigger acidification and subsequent trace metal release. Quantifying shifts in hydrological regime and connectivity dynamics across wetlands is critical for understanding the resilience of these GDEs to anthropogenic impacts. Seasonal water balances for a wetland severely impacted by drainage and acidification were combined with laboratory geochemical data and field observations to develop a conceptual model describing hydrological connectivity across the wetland. The data indicated that, with the onset of the dry season, the superficial aquifer was lowered, exposing sulfides that oxidized to form sulfuric acid and dissolving metal salts. The following dry season enhanced capillary action causing upwelling of oxidized products to the surface where evaporative precipitation created acidity scalds. Subsequent winter rainfall and infiltration caused groundwater levels to rise, intersect with the ground surface, and form disconnected acidic pools. As the wet season progressed, connectivity was established between the pools, resulting in metal-rich acid discharge from the wetland. The degree of acid fluxes and metal release was controlled by the physicochemical characteristics of the soils, its exposure to the seasonally variable wetland hydrology, antecedent hydrological conditions, hydrological connectivity (both vertical and horizontal), and the resulting biogeochemical conditions.