Sub-Saharan Africa (SSA) is strongly affected by flood hazards, endangering human lives and economic stability. However, the role of internal climate modes of variability in driving fluctuations in SSA flood occurrence remains poorly documented and understood. To address this gap, we quantify the relative and combined contribution of large-scale climate drivers to seasonal and regional flood occurrence using a new 65-year daily streamflow dataset, sea-surface temperatures derived from observations, and 12 Single Model Initial-condition Large Ensembles (SMILEs) from the Coupled Model Intercomparison Project Phases 5 and 6. We find significant relationships between floods and large-scale climate variability across SSA, with climatic drivers accounting for 30–90 % of the variability in floods. Notably, western, central, and the summer-rain region of southern Africa display stronger teleconnections to large-scale climate variability in comparison to East Africa and the winter-rain region of South Africa, where regional circulation patterns and human activities may play a more important role. In southern and eastern Africa, floods are mainly influenced by teleconnections with the Pacific and Indian Oceans, while in western and central Africa, teleconnections with the Atlantic Ocean and Mediterranean Sea play a larger role. We also find that the number of floods is projected to fluctuate by ± 10–50 % during the 21st century in response to different sequences of key modes of climate variability. We also note that the relative contributions of large-scale climate variability to future flood risks are generally consistent across all SMILEs. Our findings thus provide valuable information for long-term disaster risk reduction and management.