Shallow lakes, particularly those in low-lying areas of the subtropics, are highly vulnerable to changes in climate associated with global warming. Many of these lakes are in tropical cyclone strike zones and they experience high inter-seasonal and inter-annual variation in rainfall and runoff. Both of those factors strongly modulate sediment–water column interactions, which play a critical role in shallow lake nutrient cycling, water column irradiance characteristics and cyanobacterial harmful algal bloom (CyanoHAB) dynamics. We illustrate this with three examples, using long-term (15–25 years) datasets on water quality and plankton from three shallow lakes: Lakes Okeechobee and George (Florida, USA) and Lake Taihu (China). Okeechobee and Taihu have been impacted repeatedly by tropical cyclones that have resulted in large amounts of runoff and sediment resuspension, and resultant increases in dissolved nutrients in the water column. In both cases, when turbidity declined, major blooms of the toxic CyanoHAB Microcystis aeruginosa occurred over large areas of the lakes. In Lake George, periods of high rainfall resulted in high dissolved color, reduced irradiance, and increased water turnover rates which suppress blooms, whereas in dry periods with lower water color and water turnover rates there were dense cyanobacteria blooms. We identify a suite of factors which, from our experience, will determine how a particular shallow lake will respond to a future with global warming, flashier rainfall, prolonged droughts and stronger tropical cyclones.