Coastal waters (including estuaries and lagoons) constitute the interface between the marine and the freshwater environments, and between the continents and the oceans. Estuaries are broad portions of rivers or streams near their outlet, influenced by the marine water body into which they flow. As such, estuaries are semi-enclosed coastal bodies of brackish water with free connection to the open sea.
The demarcation between an estuary and the sea is generally the mean tidal level. Similar to coastal ponds or lakes, lagoons are shallow brackish water bodies with one or more restricted outlets to the sea. Estuaries and most lagoons receive water from land and therefore can be heavily impacted by land-based sources of pollution through inland runoffs. Coastal waters are the main area of development for artisanal fisheries and play a key role as nursery grounds for a wide range of marine species and are the principle cause of conflict between artisanal and industrial fisheries.
Coral reefs are the dominant type of ecosystems in tropical areas with low upwelling or freshwater inputs. Coral reef ecosystems occur in areas where sunlight can reach reef-building corals on solid surfaces and stable sediments. They are fragile, vital for island countries, richest in biodiversity and heavily impacted by inland runoffs and inland activities (e.g. deforestation or inappropriate agricultural practices). Coral reefs are particularly sensitive to destructive fishing methods using explosives and poisons. They are mainly used by artisanal fisheries.
Soft-bottom continental shelves
Soft-bottom continental shelves appear in front of major river systems and deltas from which they receive their characteristic fine sediments (e.g. gravel, sand and mud). Extending up to a depth of 200 metres, they are usually strongly influenced by the riverine effluents from which they draw their high productivity and which govern their natural variability. These ecosystems are exploited with a variety of fishing methods and are particularly suitable for bottom trawling. Artisanal fisheries are generally restricted to the shallower areas of these shelves, while semi-industrial and industrial fleets (with which artisanal fisheries often conflict) can exploit both the nearshore and offshore areas.
Upwelling continental shelves
Upwelling continental shelves are very productive continental shelves found mostly at the eastern boundaries of the oceans, often in front of arid zones or deserts. The usually wind-driven, upwelling process brings cold, nutrient-rich water from deep layers into the euphotic zone where photosynthesis uses sunlight and the upwelled nutrients to produce the organic matter that is the basis of the marine food chain. These ecosystems are affected by strong interannual variability (e.g. El Niño and La Niña, off Peru-Chile). They represent areas of especially high concentrations of small pelagic species usually exploited by surface fisheries using purse seiners and mid-water trawls.
Open oceans represent the largest area and volume of marine ecosystems, although their biological and fisheries production per unit of area is far less than the other ecosystems. The depth of open oceans varies from about 200m, where in theory the continental shelf ends and the continental slope starts, to 11 500m in the deepest trenches. Seamounts are noticeable elements of the open ocean ecosystem and host some long-living and fragile deep-sea resources (e.g. orange roughies) on which fisheries have recently expanded - causing concern for the conservation of these poorly-known ecosystems. Upper layers are exploited mainly with wide opening midwater trawls (e.g. for horse mackerel) and longlines (e.g. for tuna, billfishes and sharks).
Polar oceans (i.e. the Arctic and Antarctic oceans) are particular, highly-productive ecosystems with great seasonality, characterized by active, current-driven, enrichment processes that sustain important fishery resources (e.g. fish, krill, whales, small cetaceans) and other species (e.g. seabirds, seals). Some doubts have been raised that in some years krill production might be insufficient to support the demand of seals, penguins and albatross for the food needed to raise their offspring.