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Climate change will impact rural livelihoods in Southern Africa in unprecedented ways. Successful responses must account for intersecting social and ecological factors that determine natural resource access for people living in changing social-ecological systems. However, much of the existing scholarly literature treats natural resource access as a dynamic social process, while often failing to account for how it is also ecologically variable. The social-ecological systems literature more holistically considers social and ecological aspects of resource use, but rarely considers how livelihoods themselves are social-ecological. This paper advances the argument that livelihoods are a useful entry point for understanding the complex and intersecting social-ecological factors that impact natural resource use. Findings are presented from a mixed-methods research project in the variable wetland environment of the Okavango Delta of Botswana to show how participation in various fishing practices is determined by a complex combination of flooding variability, environmental governance, and social relations tied to gender and ethnicity. This article contributes to the literatures on natural resource access and social-ecological systems, increases knowledge about rural livelihoods in Botswana, and provides broader insight into how governance of social-ecological livelihood systems throughout southern Africa are likely to be challenged by climate change.