The St Lucia Estuary is part of the iSimangaliso Wetland Park, South Africa’s first UNESCO World Heritage Site, and is the largest estuarine system in Africa. This three-lake complex is particularly vulnerable to droughts and hypersaline conditions due to its large surface area (350 km2) and shallow water depth (average depth 0.9 m). A widespread bloom of the unicellular cyanobacterium Cyanothece sp. appeared in June 2009 and persisted for 18 months within the two northern basins of St Lucia (False Bay and North Lake). This was the first recorded bloom of this genus globally.