Freshwater biology is the scientific biological study of freshwater ecosystems and is a branch of limnology. This field seeks to understand the relationships between living organisms in their physical environment. These physical environments may include rivers, lakes, streams, ponds, reservoirs, or wetlands. Knowledge from this discipline is also widely used in industrial processes to make use of biological processes involved with sewage treatment and water purification. Water presence and flow is an essential aspect to species distribution and influences when and where species interact in freshwater environments.

In the UK, the Freshwater Biological Association based near Windermere in Cumbria was one of the early institutions to research the biology of freshwater and promote the concepts of trophism in lakes and demonstrated the process of migration from oligotrophic water through mesotrophic to marsh.

Freshwater biology is also used to study the effects of climate change and increased human impact on both aquatic systems and wider ecosystems. Freshwater organisms, vertebrates especially, appear to be at a higher extinction risk from climate change than terrestrial or marine organisms.

Freshwater habitats support a wide variety of organisms with habitats including rivers, streams, lakes, ponds, and wetlands.

Running water is a type of freshwater habitat that mainly consists of rivers and streams. Running, fast-moving waters have a higher oxygen content, allowing different species to thrive and making pollution easier to combat. Running water is an open system, meaning it is not isolate and exchanges matter and energy with other systems. Being an open system, a lot of organic matter found in running water is from land runoff or further sediment upstream and this matter is an important source of food for many species. Flowing bodies of water begin at the headwaters, which include springs, lakes, and snowmelt,  and travel to their mouths, typically another moving water channel or the ocean. The characteristics of the streams and rivers change throughout their journey from the source to the mouth. For example, the water at the source is clearer, has a higher oxygen content, lower temperatures, and heterotrophs common species. In the middle, the width usually expands and the species diversity increases due to temperature and oxygen content changes, including aquatic green plants and algae. The water at the mouth has a lower oxygen concentration and is murkier due to the sediment that has been collected and traveled along the length of the river or stream. This increased sediment decreases the amount of light that is able to penetrate the water and there is less diversity of flora and the lower oxygen lowers the diversity of fauna.

The riparian zone is the area along a riverbank or streambank that is home to vital, high moisture plants. These plants create a buffer between the land and the running water system, protecting it from pollution and flooding. Additionally, these plants provide a large habitat for many wetland species, a large number of which are endangered or threatened. Lastly, riparian plants shade the water from sunlight, reducing the heat stress on the water and aquatic life, while also providing nutrients in the form of organic matter.

Standing water is a type of freshwater habitat that mainly consists of lakes and ponds. This habitat has limited species diversity because they are isolated from one another and other water systems, unlike running water. Standing water experiences the process of stratification, which is when water is layered due to the oxygen content. Stratification does not occur in running water because of the fast moving water that mixes water with varying oxygen content together. The topmost layer has the most oxygen and as depth increases, the oxygen decreases. Stratification can be physically felt in the temperature of the water, as the uppermost layer of water is warmer than deeper water because it has been heated by the sun.

Standing water can be divided into three zones based on depth and distance from shore. The littoral zone is the uppermost layer and the warmest water found in lakes and ponds, as the sun directly heats is. This zone hosts the most biodiversity in standing water, with a wide variety of organisms found here, vital to the health of the ecosystem and an important aspect of the diet of organisms in the habitat, like algae, aquatic plants, clams, insects, fish, crustaceans, and amphibians. The limnetic zone is found below the littoral zone. This zone has lower temperatures, is fairly well-lit, and is occupied by a smaller variety of organisms, including phytoplankton, zooplankton, and fish. The plankton found in this zone play a crucial role in the food web of the habitat and support the diet of many important organisms. The deepest zone is the profundal zone, with very little light, colder temperatures, and higher density than the previous layers. When plankton die they fall into this layer and provide nutrients to the fauna that live in this layer. These faunas are called heterotrophs, meaning they eat dead organisms and use oxygen for cellular respiration, resulting in lower oxygen content in the profundal zone.