While climate change has been shown to impact several life‐history traits of wild‐living animal populations, little is known about its effects on dispersal and connectivity. Here, we capitalize on the highly variable flooding regime of the Okavango Delta to investigate the impacts of changing environmental conditions on the dispersal and connectivity of the endangered African wild dog (Lycaon pictus). Based on remote sensed flood extents observed over 20 years, we derive two extreme flood scenarios: a minimum and a maximum flood extent, representative of very dry and very wet environmental periods. These conditions are akin to those anticipated under increased climatic variability, as it is expected under climate change. Using a movement model parameterized with GPS data from dispersing individuals, we simulate 12,000 individual dispersal trajectories across the ecosystem under both scenarios and investigate patterns of connectivity. Across the entire ecosystem, surface water coverage during maximum flood extent reduces dispersal success (i.e., the propensity of individuals to disperse between adjacent subpopulations) by 12% and increases dispersal durations by 17%. Locally, however, dispersal success diminishes by as much as 78%. Depending on the flood extent, alternative dispersal corridors emerge, some of which in the immediate vicinity of human‐dominated landscapes. Notably, under maximum flood extent, the number of dispersing trajectories moving into human‐dominated landscapes decreases by 41% at the Okavango Delta's inflow, but increases by 126% at the Delta's distal end. This may drive the amplification of human–wildlife conflict. While predicting the impacts of climate change on environmental conditions on the ground remains challenging, our results highlight that environmental change may have significant consequences for dispersal patterns and connectivity, and ultimately, population viability. Acknowledging and anticipating such impacts will be key to effective conservation strategies and to preserve vital dispersal corridors in light of climate change and other human‐related landscape alterations.