Coastal wetlands are hotspots for biodiversity and biological productivity, yet the hydrology and carbon cycling within these systems remains poorly understood due to their complex nature. By using a novel spatiotemporal approach, this study quantified groundwater discharge and the related inputs of acidity and CO2 along a continuum of a modified coastal acid sulphate soil (CASS) wetland, a coastal lake and an estuary under highly contrasting hydrological conditions. To increase the resolution of spatiotemporal data and advance upon previous methodologies, we relied on automated observations from four simultaneous time-series stations to develop multiple radon mass balance models to estimate groundwater discharge and related groundwater inputs of acidity and dissolved inorganic carbon (DIC), along with surface water to atmosphere CO2 fluxes. Spatial surveys indicated distinct acid hotspots with minimum surface water pH of 2.91 (dry conditions) and 2.67 (flood conditions) near a non-remediated (drained) CASS area. Under flood conditions, groundwater discharge accounted for ∼14.5 % of surface water entering the lake. During the same period, acid discharge from the acid sulphate soil section of the continuum produced ∼4.8 kg H2SO4 ha−1 day−1, a rate much higher than previous studies in similar systems. During baseflow conditions, the low pH water was rapidly buffered within the estuarine lake, with the pH increasing from 4.22 to 6.07 over a distance of ∼250 m. The CO2 evasion rates within the CASS were extremely high, averaging 2163 ± 125 mmol m−2 day−1 in the dry period and 4061 ± 259 mmol m−2 day−1 under flood conditions. Groundwater input of DIC could only account for 0.4 % of this evasion in the dry conditions and ∼5 % during the flood conditions. We demonstrated that by utilising a spatiotemporal (multiple time-series stations) approach, the study was able to isolate distinct zones of differing hydrology and biogeochemistry, whilst providing more reasonable groundwater acid input estimates and air–water CO2 flux estimates than some traditional sampling designs. This study highlights the notion that modified CASS wetlands can release large amounts of CO2 to the atmosphere because of high groundwater acid inputs and extremely low surface water pH.