An aquatic ecosystem is an ecosystem in a body of water. Communities of organisms that are dependent on each other and on their environment live in aquatic ecosystems. The two main types of aquatic ecosystems are marine ecosystems and freshwater ecosystems.

Marine ecosystems cover approximately 71% of the Earth's surface and contain approximately 97% of the planet's water. They generate 32% of the world's net primary production. They are distinguished from freshwater ecosystems by the presence of dissolved compounds, especially salts, in the water. Approximately 85% of the dissolved materials in seawater are sodium and chlorine. Seawater has an average salinity of 35 parts per thousand (ppt) of water. Actual salinity varies among different marine ecosystems.

Marine ecosystems can be divided into many zones depending upon water depth and shoreline features. The oceanic zone is the vast open part of the ocean where animals such as whales, sharks, and tuna live. The benthic zone consists of substrates below water where many invertebrates live. The intertidal zone is the area between high and low tides; in this figure it is termed the littoral zone. Other near-shore (neritic) zones can include estuaries, salt marshes, coral reefs, lagoons and mangrove swamps. In the deep water, hydrothermal vents may occur where chemosynthetic sulfur bacteria form the base of the food web.