Coal seam gas (CSG, or coal bed methane) mining is rapidly growing, with poorly understood impacts on groundwater and surface water systems. Here, we use chemical tracers to investigate groundwater-surface water connectivity in an Australian river system (Richmond River Catchment, New South Wales) prior to CSG extraction but after ∼ 50 exploratory CSG wells were drilled. We performed four surveys of 29 interconnected creek and river sites, over contrasting hydrological conditions. Radon was used to determine if a surface water segment was gaining groundwater. Radon observations over four seasons revealed that 28 out of 77 surface water segments were clearly gaining groundwater, 5 were possibly gaining groundwater and 44 were undetermined. This is equivalent to gaining segments in 333 km (39%) of surface water from the 864 km being investigated. High spatial and temporal variability in groundwater gaining segments was found. Na/Cl ratios were used to determine the fraction of groundwater in surface water. Overall, the groundwater contribution in surface waters was 14–24% higher in post flood conditions than during the other three surveys of baseflow and moderate flow conditions. The results serve as a regional baseline assessment of river water chemistry and groundwater-surface water connectivity prior to the planned development of CSG fields. Our geochemical tracer approach allows for a quick qualitative assessment of groundwater-surface water connectivity in poorly gauged river systems and can define priority locations where groundwater extraction for CSG mining should be carefully managed.