Floodplain rivers in arid and semi-arid regions may be the most threatened of all river systems because water resource developments typically dampen their most distinctive characteristics-extreme flow variability and 'boom and bust' ecological dynamics. This article shows how one of the world's most variable arid-zone river systems-Cooper Creek in Australia's Lake Eyre Basin-functions and how it supports its unique fish assemblage and productive fisheries. The ecological roles of drought refugia, channel flows and flooding are reviewed in relation to fish persistence and losses, life history strategies, movement potential, food web processes and production levels. Comparisons are drawn with other floodplain rivers and fisheries to draw out common understandings and universal principles for conservation and management of arid-zone rivers and their fish resources. Ecological implications of hydrologic alterations and land-based activities are presented to highlight the importance of maintaining the hydrologic, geomorphic, sedimentary and biogeochemical processes of arid-zone river systems. Preservation or restoration of natural flow intermittency, sequential flood pulses, complex habitat mosaics, connectivity and identification of the environmental flow requirements for highly valued species and processes are key scientific principles for the management of arid-zone floodplain rivers.