Aquatic biomes are divided into two types based on salinity: marine and freshwater. Salinity refers to the concentration of salt in the biome. Marine biomes, like oceans and seas, are very salty. Freshwater biomes have very low levels of salt. Estuaries are marine biomes that are found where freshwater (for example, a river) meets salt water (the ocean). Estuaries have a range of salinity. Salinity is the most important factor in the divide between types of aquatic biomes because salt balance is essential for cell function, and therefore, an organism's survival. Freshwater organisms cannot survive in marine biomes and vice versa.

Another abiotic factor in aquatic biomes is the depth of water. Light can only penetrate water to a certain depth (for example, an average of 262 feet--80 meters--in the ocean). Light is essential for photosynthesis, just as in terrestrial biomes. Therefore, water that is very deep or turbid (cloudy) will likely have less plant life. Depth also affects temperature: Deeper waters tend to be cooler.

Aquatic biomes are also characterized by whether the water in them is moving or not. Moving water, especially white water, tends to have a higher concentration of oxygen in it than very still water. This is because as water tumbles over rocks, air and water molecules mix. However, fast moving water can also prevent organisms from establishing a habitat and can push important nutrients by too quickly for organisms to use them.

Plants need nutrients like nitrogen and phosphorous. These nutrients cycle into animals as the animals consume the plants. A limited amount of nutrients can limit the ability of plants to complete photosynthesis. Therefore, nutrient availability also has an important effect on a biome.