We investigated the paradox of why Amazonian manatees Trichechus inunguis undergo seasonal migrations to a habitat where they apparently fast. Ten males were tracked using VHF telemetry between 1994 and 2006 in the Mamirauá and Amanã Sustainable Development Reserves, constituting the only long-term dataset on Amazonian manatee movements in the wild. Their habitat was characterized by analysing aquatic space and macrophyte coverage dynamics associated with the annual flood-pulse cycle of the River Solimões. Habitat information came from fieldwork, two hydrographs, a three-dimensional model of the water bodies and classifications of Landsat-TM/ETM+ images. We show that during high-water season (mid-May to end-June), males stay in várzea lakes in association with macrophytes, which they select. We then show that, during low-water (October–November), the drastic reduction in aquatic space in the várzea leads to the risk of their habitat drying out and increases the manatees' vulnerability to predators such as caimans, jaguars and humans. This explains why males migrate to Ria Amanã. Based on data on illegal hunting, we argue that this habitat variability influences females to migrate too. We then use published knowledge of the environment's dynamics to argue that when water levels are high, the habitats that can support the largest manatee populations are the várzeas of white-water rivers, and we conjecture that rias are the species' main low-water refuges throughout Western Amazonia. Finally, we warn that the species may be at greater risk than previously thought, because migration and low-water levels make manatees particularly vulnerable to hunters. Moreover, because the flooding regime of Amazonian rivers is strongly related to large-scale climatic phenomena, there might be a perilous connection between climate change and the future prospects for the species. Our experience reveals that the success of research and conservation of wild Amazonian manatees depends on close working relationships with local inhabitants.