Floodplain lagoons in the Queensland Wet Tropics bioregion, Australia, are important and threatened habitats for fish. As part of studies to assess their ecological condition and functions, we examined patterns of occurrence of fish larvae, juveniles and adults in 10 permanent lagoons on the Tully–Murray floodplain. Lagoons contained early life-history stages of 15 of the 21 native species present, including 11 species that complete their life cycle in fresh waters and 4 that require access to saline habitats for larval development. Lagoon connectivity to the rivers, distance from the coast and flood dynamics influenced temporal variation in fish abundance, population size structures and recruitment patterns. This study and the literature show that wet, post-wet and dry-season habitats are utilised by small opportunists (e.g. Melanotaenia splendida), an equilibrium species (Glossamia aprion) and larger periodic strategists (neosilurid catfishes). Maintenance of natural seasonal patterns of flow and connectivity, and active protection of permanent floodplain lagoons from riparian and land-use disturbance, will be essential if their roles in fish recruitment are to be sustained.