Aquatic ecosystems, inland, coastal and marine, provide humans with resources for recreation, food and livelihood. They also perform many other important environmental functions, e.g. in relation to meteorological events, pollution etc., contributing to general human well-being. They are used by both capture fisheries and aquaculture as well as other competing sectors. Achieving sustainable use of aquatic ecosystems has been the main and largely failed objective of fisheries management for decades. The formally adopted Ecosystem Approach to Fisheries (EAF) imposes further efforts in that direction, implying better understanding and better governance.

Conceptually, ecosystems can be described at various sizes and with different degrees of resolution, from the Earth or a whole ocean with their large scale relations and processes, to a microscopic grain of sand and its immediate surroundings. The choice is based on pragmatic considerations. Fisheries usually better relate to the intermediate ecosystem size range, corresponding to the size of the resources sought and of social structures in charge of their stewardship. In each case, adjustments will be needed to account for the possible mismatch between the limits of the human jurisdictions and those of the species distributions and ecological processes.

The exploited ecosystem is unavoidably affected by fishery activities. Wild or ranched stocks and other organisms affect each other e.g. through predator-prey relationships or transfer of diseases. The impact of capture or culture on the resource, the associated and dependent species, the habitat, the bottom and the benthic flora and fauna can be particularly severe and longlasting. It is also vulnerable to degradation and pollution imposed by other industries, with long-lasting or irreversible effects, including on the production of fisheries, seafood quality and fishers' livelihood.

Natural variability and climate change have significant implications for productivity and management. Catastrophic natural events (e.g. typhoons, tsunamis) have significant impact on resources, infrastructures and people. Understanding, predicting and accounting for them is a significant challenge of the next decade.