Ecosystems in semi-arid areas remain essential to securing livelihoods and aiding climate change adaptation. However, land-use and land-cover change (LULCC) is the leading driver of biodiversity, ecosystem services, habitat, and ecosystem loss in most rural areas of developing countries. We evaluated LULCC in the Bobirwa sub-district of Botswana between 1995 and 2015. We employed the supervised classification’s maximum likelihood algorithm on the 1995, 2005, and 2016 Landsat images to establish the implications of LULCC on the delivery of provisioning ecosystem services (ES) and ecosystem-based adaptation in the Limpopo Basin part of Botswana. Five major LULC classes—vegetation, cropland, bare land, built-up areas, and water bodies—were identified in the sub-district. The decline in vegetation by 50.67 km2/year between 1995 and 2016 was characterized by an increase in croplands (34.02 km2/year). These changes were attributed to the growing human population that induced farming households to expand croplands. Government programs also encouraged agricultural expansions by offering free inputs and compensating smallholder farmers for land preparation. Higher agricultural yields remained critically low while the loss of vegetated areas to croplands threatened biodiversity, habitats, and the sustainability of provisioning ES through impaired ecosystem functions. There is an urgent need to arrest all unnecessary agricultural expansions and enhance agricultural productivity from current land parcels. The government and other relevant stakeholders also need to strengthen the ecosystem management capacities of local communities and support them to develop and implement biodiversity-based village action plans. Engaging communities through participatory, biodiversity-based action planning promotes biodiversity conservation and the sustainable use of ecosystem resources.