Tree cover differentiates forests from savannas and grasslands. In tropical floodplains, factors differentiating these systems are poorly known, even though floodplains cover 10% of the tropical landmass. Seasonal inundation potentially presents trees with both challenges (soil anoxia) and benefits (moisture and nutrient deposition), the relative importance of which may depend on ecological context, e.g. if floods alleviate water stress more in more arid ecosystems. Here, we use remotely sensed data across 13 large tropical and sub-tropical floodplain ecosystems on five continents to show that climatic water balance (i.e. precipitation—potential evapotranspiration) strongly increases floodplain tree cover in interaction with flooding, fire and topography. As predicted, flooding increases tree cover in more arid floodplains, but decreases tree cover in climatically wetter ones. As in uplands, frequent fire reduced tree cover, particularly in wet regions, but—in contrast with uplands—lower elevation and sandier soils decreased tree cover. Our results suggest that predicting the impacts of changing climate, land use and hydrology on floodplain ecosystems depends on considering climate-disturbance interactions. While outright wetland conversion proceeds globally, additional anthropogenic activities, including alteration of fire frequencies and dam construction, will also shift floodplain tree cover, especially in wet climates.