Climate change and variability pose significant threats to southern Africa, with projected continuous drought in Botswana. This study examines the causal relationships between African-Indian monsoon systems (East Africa, West Africa, and Peninsula India), the Mascarene High, and interannual rainfall variability over Botswana. Using statistical analysis and mapping techniques (Pearson correlation statistics and convergent cross mapping (CCM)), the authors analysed the impact of these weather systems on rainfall variability from 1979 to 2021. The findings reveal significant negative associations between these weather systems and interannual rainfall variability in Botswana, shedding light on their crucial roles in shaping the region's rainfall patterns. Bidirectional causation between different regions and the Mascarene High was observed, emphasising the interconnectedness of rainfall patterns. Significant findings include the bidirectional causation between Botswana and West Africa rainfall during March–May (MAM) and October–December (OND) seasons. In addition, the authors also observed bidirectional causation between Botswana and Peninsula Indian rainfall during the OND season. The study highlights the potential of these factors in predicting extreme events and assists in planning for potential risks associated with rainfall variability in Botswana to promote community awareness and education on climate change and variability, water conservation, and sustainable livelihood.