A comprehensive river basin assessment is key to integrated land and water resources management (ILWRM), which is based on an integrated system analysis to identify interacting hydrological processes that are driven by landscape features and socioeconomic development. Software toolsets like RBIS (River Basin Information System), GRASS-HRU, and the hydrological modelling system JAMS/J2000 were used and further developed for basin assessments and modelling of hydrological process dynamics and other environmental processes in selected catchments in southern Africa. These are the Gaborone Dam catchment (Botswana, South Africa), the Verlorenvlei catchment (South Africa), and the Luanginga catchment (Angola, Zambia). All of these catchments respond very sensitively to changes in climate and land management, revealing additional issues like a strong decline of inflow (Gaborone Dam) or a decline of usable groundwater resources (Verlorenvlei). Further, extensive wetland areas in the Upper Zambezi (Luanginga) respond strongly to changes in hydroclimatic conditions and land management. In this study, newly developed and improved simulation components for representing processes with a strong local impact on the hydrological conditions such as floodplain inundation, irrigation, small farm dams, and contour bank farming were used to more precisely simulate the hydrology of the respective basins. After successful model validation and an improved understanding of catchment dynamics, the models were used as a platform for different land or climate change analysis. Taking the RCP 8.5 scenario based on EC-Earth and ECHAM, downscaled by REMO, into account, the Luanginga catchment showed a strong decrease in runoff generation, inundation extent, and groundwater recharge. For the Kruismannsrivier, a sub-catchment of the Verlorenvlei, the relation between contour farming and related effects on surface/subsurface runoff processes and related parameters were revealed through modelling. These findings could also be projected to the Gaborone Dam catchment, in which the influence of small farm dams spread over the catchment could be shown by modelling.