Significant commercial and recreational activities rely on Australia's freshwater fisheries resource. This resource has severely declined in recent years with even the survival of several fish species being threatened. There is currently little coordination of Australia s freshwater fisheries management and research is dominated by perceptions in individual States or Territories. Water and land management agencies, other than those with specific responsibility for fisheries, influence the major issues impacting the sustainability of freshwater fisheries. This article identifies and prioritises the six major threats to the sustainability of Australia's freshwater fisheries resource, based on information gathered from one survey and two expert panels, and suggests research needed to address those threats. The major threats are (1) habitat degradation, (2) pollution, (3) reduced environmental flows, (4) barriers to migration, (5) introduced species and (6) fishing. The commonality of research needs between these six threats and within components of each major threat is stressed. Greater coordination of fisheries, water and land management agencies both between and within States and Territories is required.