Droughts are widespread natural hazards and in many regions their frequency seems to be increasing. A finer-resolution version (0.05° × 0.05°) of the continental-scale hydrological model PCRaster Global Water Balance (PCR-GLOBWB) was set up for the Limpopo River basin, one of the most water-stressed basins on the African continent. An irrigation module was included to account for large irrigated areas of the basin. The finer resolution model was used to analyse hydrological droughts in the Limpopo River basin in the period 1979-2010 with a view to identifying severe droughts that have occurred in the basin. Evaporation, soil moisture, groundwater storage and runoff estimates from the model were derived at a spatial resolution of 0.05° (approximately 5 km) on a daily timescale for the entire basin. PCR-GLOBWB was forced with daily precipitation and temperature obtained from the ERA-Interim global atmospheric reanalysis product from the European Centre for Medium-Range Weather Forecasts. Two agricultural drought indicators were computed: the Evapotranspiration Deficit Index (ETDI) and the Root Stress Anomaly Index (RSAI). Hydrological drought was characterised using the Standardized Runoff Index (SRI) and the Groundwater Resource Index (GRI), which make use of the streamflow and groundwater storage resulting from the model. Other more widely used meteorological drought indicators, such as the Standardized Precipitation Index (SPI) and the Standardized Precipitation Evaporation Index (SPEI), were also computed for different aggregation periods. Results show that a carefully set-up, process-based model that makes use of the best available input data can identify hydrological droughts even if the model is largely uncalibrated. The indicators considered are able to represent the most severe droughts in the basin and to some extent identify the spatial variability of droughts. Moreover, results show the importance of computing indicators that can be related to hydrological droughts, and how these add value to the identification of hydrological droughts and floods and the temporal evolution of events that would otherwise not have been apparent when considering only meteorological indicators. In some cases, meteorological indicators alone fail to capture the severity of the hydrological drought. Therefore, a combination of some of these indicators (e.g. SPEI-3, SRI-6 and SPI-12 computed together) is found to be a useful measure for identifying agricultural to long-term hydrological droughts in the Limpopo River basin. Additionally, it was possible to undertake a characterisation of the drought severity in the basin, indicated by its time of occurrence, duration and intensity.