Water development threatens rivers and their biodiversity. Amphidromous shrimp are particularly vulnerable as they require migration between freshwater and estuaries to complete their life cycle. The Fitzroy River is a large tropical intermittent river undergoing water development that is home to the amphidromous shrimp Macrobrachium spinipes (cherabin), yet little is known about its habitat use and flow‐ecology making it difficult to inform sustainable water‐take. We investigated habitat associations, distributional patterns suggestive of amphidromy, and the influence of water availability by sampling main channel and floodplain pools along a 350‐km river length during 2 contrasting flow years. Applying a size‐specific abundance model, we estimated abundance per size class, site, and year. We then predicted abundance at the landscape scale with remotely sensed water to reveal the impact of water availability on the meta‐population. Our model revealed that juveniles were in greatest abundance in downstream main channel pools, whereas adults were in greatest abundance in upstream floodplain pools. Abundance varied by year with lower numbers predicted in the low‐flow year. Longitudinal and habitat patterns remained when our pool‐level results were scaled to the landscape, and the positive relationship of abundance to wet‐season flow was strengthened. The predominance of smaller cherabin in the lower reaches of the river provides indirect support for an estuarine nursery and amphidromous life history; however, small individuals observed in landlocked pools, during late dry season suggests possible within‐river recruitment. The importance of water development policies that protect wet‐season flow and passage along the Fitzroy River is supported by this work. These types of policies are likely to be important for this and other amphidromous shrimp species across Australia, Southeast Asia and further afield. Further research detailing the species life history and describing flow–recruitment relationships will be important contributions to understanding this important taxonomic group and refining policies for current and future water resource development.