Aquatic ecosystems include both saltwater and freshwater biomes. The abiotic factors important for the structuring of aquatic ecosystems can be different than those seen in terrestrial systems. Sunlight is a driving force behind the structure of forests and also is an important factor in bodies of water, especially those that are very deep, because of the role of photosynthesis in sustaining certain organisms. Density and temperature shape the structure of aquatic systems.

Oceans may be thought of as consisting of different zones based on water depth and distance from the shoreline and light penetrance. Different kinds of organisms are adapted to the conditions found in each zone. Coral reefs are unique marine ecosystems that are home to a wide variety of species. Estuaries are found where rivers meet the ocean; their shallow waters provide nourishment and shelter for young crustaceans, molluscs, fishes, and many other species.

Freshwater biomes include lakes, ponds, rivers, streams, and wetlands. Bogs are an interesting type of wetland characterized by standing water, lower pH, and a lack of nitrogen.