Future increases in the intensity of hurricanes and El Niño periods predicted by climate change models have focused attention on their role in stimulating harmful algal blooms (HABs). A series of hurricanes that recently impacted Florida (USA) provided a unique opportunity to explore the relationships between hurricanes, El Niño and HABs in two Florida estuaries subject to repeated intense ecosystem disruptive HABs, the Indian River Lagoon and the St. Lucie Estuary. The roles that hurricanes and El Niño play in contributing to HAB events are examined in the context of key structural and functional features of each estuary and their watersheds, including morphology, water residence time and hydrology, such as the influence of Lake Okeechobee discharges into the St. Lucie Estuary. The most direct impact was the increase in rainfall associated with hurricanes and El Niño, resulting in enhanced nutrient loads which drive HABs in the Indian River Lagoon and Lake Okeechobee. Major HABs in Lake Okeechobee also present an indirect threat of freshwater HAB blooms in the St. Lucie Estuary via mandated discharges from the lake into the estuary during high rainfall periods. Conversely, during the absence of HABs in Lake Okeechobee, short water residence times produced by discharges into the St. Lucie Estuary can result in lower bloom intensities.