Freshwater ecosystems are a subset of Earth's aquatic ecosystems that include the biological communities inhabiting freshwater waterbodies such as lakes, ponds, rivers, streams, springs, bogs, and wetlands. They can be contrasted with marine ecosystems, which have a much higher salinity. Freshwater habitats can be classified by different factors, including temperature, light penetration, nutrients, and vegetation.

There are three basic types of freshwater ecosystems: lentic (slow moving water, including pools, ponds, and lakes), lotic (faster moving streams, for example creeks and rivers) and wetlands (semi-aquatic areas where the soil is saturated or inundated for at least part of the time). 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 (for example cholera outbreaks due to sewage contamination). 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 (macroinvertebrates, macrophytes and fish) 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. Climate change is putting further pressure on these ecosystems because water temperatures have already increased by about 1 °C, and there have been significant declines in ice coverage which have caused subsequent ecosystem stresses.

There are three basic types of freshwater ecosystems: Lentic (slow moving water, including pools, ponds, and lakes), lotic (faster moving water, for example streams and rivers) and wetlands (areas where the soil is saturated or inundated for at least part of the time). Limnology (and its branch freshwater biology) is the study of freshwater ecosystems.

River ecosystems are flowing waters that drain the landscape, and include the biotic (living) interactions amongst plants, animals and micro-organisms, as well as abiotic (nonliving) physical and chemical interactions of its many parts. River ecosystems are part of larger watershed networks or catchments, where smaller headwater streams drain into mid-size streams, which progressively drain into larger river networks. The major zones in river ecosystems are determined by the river bed's gradient or by the velocity of the current. Faster moving turbulent water typically contains greater concentrations of dissolved oxygen, which supports greater biodiversity than the slow-moving water of pools. These distinctions form the basis for the division of rivers into upland and lowland rivers.

The food base of streams within riparian forests is mostly derived from the trees, but wider streams and those that lack a canopy derive the majority of their food base from algae. Anadromous fish are also an important source of nutrients. Environmental threats to rivers include loss of water, dams, chemical pollution and introduced species. A dam produces negative effects that continue down the watershed. The most important negative effects are the reduction of spring flooding, which damages wetlands, and the retention of sediment, which leads to the loss of deltaic wetlands.

A wetland is a distinct semi-aquatic ecosystem whose groundcovers are flooded or saturated in water, either permanently, for years or decades, or only seasonally. Flooding results in oxygen-poor (anoxic) processes taking place, especially in the soils. Wetlands form a transitional zone between waterbodies and dry lands, and are different from other terrestrial or aquatic ecosystems due to their vegetation's roots having adapted to oxygen-poor waterlogged soils. They are considered among the most biologically diverse of all ecosystems, serving as habitats to a wide range of aquatic and semi-aquatic plants and animals, with often improved water quality due to plant removal of excess nutrients such as nitrates and phosphorus.