In Australia, native vegetation clearance has had considerable impacts on surface water and groundwater salinities. The impact on surface water-groundwater connectivity is less understood. Ahydraulic, hydrochemical, and tracer-based study was conducted at two contrasting fractured rock catchments in South Australia. Results indicate that connectivity was variable across each of the catchments. The influence of the fractured rock aquifer was minimal in the pristine, uncleared Rocky River catchment, whereas in the cleared, mixed land-use Cox Creek catchment, the fractured rock aquifer played a more significant role. The results emphasise the need to understand the importance that the impacts of land-use change (particularly vegetation clearance) can have on surface water-groundwater connectivity.