This study investigated the environmental factors influencing the distribution of the endangered arapaima (Arapaima spp.) in floodplains of the Amazon. The abundance of arapaima was found to be positively related to the area and depth of the water column, and hence volume of lakes. Greater depth of water column also was related positively with the abundance and presence of arapaima in connecting channels. The abundance of arapaima was positively related to the connectivity of the lake with other water bodies. The principal reason for arapaima to prefer habitats that are deep, large, and connected to other water bodies appears to be increased survival through lower susceptibility to extreme drought events and increased mobility and availability of food resources. Deeper, larger, and more connected lakes and connecting channels sustain greater arapaima populations; they can now be used to prioritize conservation efforts.