Determining the sustainability of groundwater use in drylands with high climate variability is complex. Central to this determination is an understanding of groundwater recharge and associated processes and controls. Groundwater recharge in drylands can occur by diffuse and focused recharge (focused recharge being associated with intense episodic rainfall events and ephemeral river flow, predicted to increase and intensify with climate change). This study evaluated the relative significance and dominant controls on these two recharge processes. Ten groundwater hydrographs with multidecadal observations were collated from the Limpopo Province, South Africa, based on their proximity to river channels and rain gauges, representing diversity in local climate, landscape, vegetation, and hydrogeological conditions. The hydrographs showed that groundwater-level rises are sensitive to rainfall intensity during the rainy season, with generally larger increases after years with large episodic rainfall events, which disproportionately contribute to groundwater replenishment. Recharge processes and annual recharge volumes were quantified using the water-table fluctuation method and the numerical model HYDRUS-1D. This allowed for the inference of additional recharge contributions from focused recharge in proximity to ephemeral rivers, up to a factor of five relative to diffuse recharge. The analysis revealed synchronicity and linear correlation between annual river discharge and recharge close to the river, substantiating the importance of focused recharge close to the river network. The study showed that recharge in drylands is subject to large spatial and temporal variation and that consideration of focused and episodic recharge is critically important for managing groundwater resources at various scales in these regions.