The spatial and temporal structures of waterbird communities are dynamic and complex with many driving factors. We used long-term waterbird census data at two lakes in Zimbabwe to explore the ecological and anthropogenic drivers of waterbird community composition and abundance. Ecological drivers predicted to influence waterbird communities include rainfall quantity and distribution, waterbird movement, breeding and moulting; anthropogenic drivers include activities such as fishing and agriculture. Results suggest that seasonal variations in resource availability influenced the waterbird community composition and abundance, as did movements at local, regional, and intercontinental scales. Bird numbers in the two perennial lakes experienced large changes in structure during two droughts. We also used the study as a baseline for considering the risk of spread of avian influenza virus (AIV) spread in waterbird communities in Zimbabwean lakes, which is likely to be higher in dry seasons and during drought years when waterbird abundance is high. Our study emphasises the importance of long-term ecological data in understanding crucial aspects of biodiversity conservation as well as pathogen dynamics in wild waterbird communities, with important management implications.