Freshwater ecosystems are a subset of Earth's aquatic ecosystems. They include lakes, ponds, rivers, streams, springs, bogs, and wetlands. They can be contrasted with marine ecosystems, which have a larger salt content. Freshwater habitats can be classified by different factors, including temperature, light penetration, nutrients, and vegetation. There are three basic types of freshwater ecosystems: Lentic, lotic and wetlands. Freshwater ecosystems contain 41% of the world's known fish species.
Freshwater ecosystems have undergone substantial transformations over time, which has impacted various characteristics of the ecosystems. Original attempts to understand and monitor freshwater ecosystems were spurred on by threats to human health. Early monitoring focused on chemical indicators, then bacteria, and finally algae, fungi and protozoa. A new type of monitoring involves quantifying differing groups of organisms and measuring the stream conditions associated with them. Threats to freshwater biodiversity include overexploitation, water pollution, flow modification, destruction or degradation of habitat, and invasion by exotic species.