1. By any measure, fishes are among the world's most important natural resources. Annual exploitation from wild populations exceeds 90 million tonnes, and fish supply over 15% of global protein needs as part of total annual trade exceeding $US 55 billion. Additionally, with over 25 000 known species, the biodiversity and ecological roles of fishes are being increasingly recognised in aquatic conservation, ecosystem management, restoration and aquatic environmental regulation.
2. At the same time, substantial management problems now affect the production, exploitable stocks, global diversity, trophic structure, habitat quality and local composition of fish communities.
3. In marine systems, key issues include the direct effects of exploitation on fish, habitats and other organisms, while habitat or water quality problems arise also from the atmospheric, terrestrial and coastal environments to which marine systems are linked. In freshwaters, flow regulation and obstruction by dams, fragmentation, catchment management, pollution, habitat alterations, exotic fish introductions and nursery-reared fish are widespread issues.
4. Management responses to the problems of fish and fisheries include aquatic reserves in both marine and freshwater habitats, and their effectiveness is now being evaluated. Policies on marine exploitation increasingly emphasise fishes as integral components of aquatic ecosystems rather than individually exploitable stocks, but the rationalisation of fishing pressures presents many challenges. In Europe, North America and elsewhere, policies on freshwaters encourage habitat protection, integrated watershed management and restoration, but pressures on water resources will cause continued change. All these management approaches require development and evaluation, and will benefit from a perspective of ecological understanding with ecologists fully involved.
5. Synthesis and applications. Although making a small contribution to the Journal of Applied Ecology in the past, leading work on aquatic problems and fish-related themes appear increasingly in this and other mainstream ecology journals. As this special profile of five papers shows, significant contributions arise on diverse issues that here include the benefit of aquatic reserves, river restoration for fish, the accumulation of contaminants, interactions with predators, and the fitness of salmonids from nurseries. This overview outlines the current context in which papers on the applied ecology of fish and fisheries are emerging, and it identifies scope for further contributions.