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Increasing temperatures and wildfire incidence and decreasing precipitation and river runoff in southern Africa are predicted to have a variety of impacts on the ecology, structure, and function of semi-arid savannas, which provide innumerable livelihood resources for millions of people. This paper builds on previous research that documents change in inundation and fire regimes in the Chobe River Basin (CRB) in Namibia and Botswana and proposes to demonstrate a methodology that can be applied to disentangle the effect of environmental variability from land management decisions on changing and ecologically sensitive savanna ecosystems in transboundary contexts. We characterized the temporal dynamics (1985–2010) of vegetation productivity for the CRB using proxies of vegetation productivity and examine the relative importance of shifts in flooding and fire patterns to vegetation dynamics and effects of the association of phases of the El Niño—Southern Oscillation (ENSO) on vegetation greenness. Our results indicate that vegetation in these semi-arid environments is highly responsive to climatic fluctuations and the long-term trend is one of increased but heterogeneous vegetation cover. The increased cover and heterogeneity during the growing season is especially noted in communally-managed areas of Botswana where long-term fire suppression has been instituted, in contrast to communal areas in Namibia where heterogeneity in vegetation cover is mostly increasing primarily outside of the growing season and may correspond to mosaic early dry season burns. Observed patterns of increased vegetation productivity and heterogeneity may relate to more frequent and intense burning and higher spatial variability in surface water availability from both precipitation and regional inundation patterns, with implications for global environmental change and adaptation in subsistence-based communities.