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Freshwater ecosystems are a subset of Earth's aquatic ecosystems. They include lakes, ponds, rivers, streams, springs, bogs, wetlands, marshes, swamps, peatland, and freshwater karst systems. Freshwater ecosystems are found on every continent on earth and cover an estimated 12,543,500-14,443,550 square kilometers globally. Freshwater habitats can be classified by many different characteristics. As such, there are many different classification schemes and definitions in the field of limnology which can make the global analysis of freshwater ecosystems difficult. Limnology is the study of freshwater ecosystems. Freshwater ecosystems have undergone substantial transformations over time, which have impacted various characteristics of these ecosystems. Broadly, freshwater ecosystems can be divided into lentic ecosystems (still water; such as lakes and ponds) and lotic ecosystems (flowing water; such as rivers and streams).

Original attempts to understand and monitor freshwater ecosystems were spurred on by threats to human health (ex. Cholera outbreaks due to sewage contamination). Early monitoring focused on chemical indicators, then bacteria, and finally algae, fungi and protozoa. Currently, a more comprehensive type of monitoring is used and involves quantifying differing groups of organisms (macroinvertebrates, macrophytes and fish) and measuring the stream conditions associated with them.

Biodiversity and Characteristics of Freshwater Ecosystems
There are countless characteristics that define freshwater ecosystems throughout the world. Freshwater ecosystems are often categorized by the differences in these characteristics. These characteristics can be split between abiotic and biotic factors and help shape the differences in freshwater ecosystems. It is important to realize that although these characteristics can be categorized for ease of understanding, many of the factors have complex interactions with each other and are unique within each ecosystem.

Abiotic Characteristics
Abiotic (non-living) factors impact the structure of freshwater ecosystems making them a vital part of each system. Freshwater ecosystem structure is dependent on natural water availability and every freshwater ecosystem is regulated by the hydrologic cycle. The availability of water in these systems is dependent on precipitation, evapotranspiration, and groundwater. Additionally, many freshwater ecosystems are impacted by water flow. Water flow is one of the major drivers creating structural differences between lentic and lotic systems, and dominates river and stream ecology. For example, streams and rivers can be characterized by non linear hydrologic patterns, whereas lakes can be characterized as being hydrologically stable with potential for lake turnover. Floodplains and wetlands are characterized by seasonal flooding, with systems having effects of both high and low water flow. In addition to the direct effects of hydrology on freshwater ecosystems, there are many related indirect factors which impact freshwater ecosystems.

One way that hydrologic features affect freshwater ecosystems indirectly is via soil moisture. Soil moisture has a huge impact on plant health within freshwater systems. Changes in soil moisture are especially important for understanding ecologic processes that occur in seasonally inundated wetlands. Hydrology also impacts the chemical composition found in freshwater ecosystems, which have a multitude of ecological effects. The chemical composition found in freshwater ecosystems determines what types of biotic organisms can thrive there. Some vital factors that impact freshwater ecology are pH, Dissolved Oxygen (DO), and nutrients. In freshwater ecosystems, the pH typically ranges from 6-9, with peat bogs and acid rain impacted lakes having a lower range of ~4-5. In some extreme cases, streams and groundwater impacted by mining activities have shown pHs of 3 or less. Although most aquatic organisms are tolerant to a range of pHs, dramatic shifts of pH in freshwater ecosystems can be detrimental. DO variation in freshwater ecosystems limits aquatic organisms habitat, this is especially important for freshwater fish species and other organisms because of their high DO requirements. Lotic systems tend to have high DO (although this is flow dependent), and lentic systems vary in DO concentration. Lake DO is dependent on depth and season, and wetland/floodplain type ecosystems typically have relatively low DO. Nutrient composition is also another factor determining ecological composition within freshwater ecosystems. Carbon, nitrogen, and phosphorous are often the most limiting nutrients in terms of aquatic biomass, in particular for photosynthetic producers. Freshwater ecosystem monitoring of nitrogen and phosphorus is especially important for the prevention of eutrophication in freshwater aquatic systems.

Biotic Characteristics
Freshwater ecosystems share the common characteristic that the area of water closest to land tends to be the most productive. Within this generalization however, freshwater ecosystems have their own distinct organizations of biota. In lakes and ponds, there are specific zones, whose abiotic characteristics determine which types of biota exist there. The majority of biodiversity in lakes and ponds is found in the littoral zone, due to the ideal conditions for photosynthesis, and more complex habitat structure because of the plant growth. Many of the primary producers of an aquatic ecosystem can be found in the littoral zone, including periphyton, phytoplankton and macrophytes. In addition to producers, there are a wide range of consumers found in the littoral zone. Snails, amphibians, crustaceans, insects and fish also thrive in this area of lakes and ponds. Venturing further into the lake depths, the limnetic or pelagic zone is reached. In this open water zone, there is still plenty of life to be seen including algae, zooplankton, insects and fish. The benthic zone is at the bottom of these different zones, and is typically dominated by invertebrate species. The biotic interactions between the trophic levels seen in each zone are highly controlled by predation in lake and pond systems. Stream biology does not see the same zonation as lakes and ponds. Streams are typically dominated by attached algae, aquatic invertebrates, and fish. Another factor that impacts the biotic characteristics of freshwater ecosystems is connectivity. In rivers and streams, there is typically high connectivity between areas, which makes recolonization by organisms easier, and hybridization possible. The lack of connectivity in lakes and ponds fosters endemism, which is why so many species are only seen in certain lakes and ponds. In freshwater ecosystems such as wetlands and floodplains, connectivity provides breeding habitats. The connectivity of freshwater systems is an example of how biotic and abiotic factors are intertwined.

Freshwater Availability and Services
Although there is a vast distribution of freshwater ecosystems throughout the world, there is a surprisingly small amount of freshwater available globally. Freshwater ecosystems account for only 0.009% of the earth's surface water, the only other freshwater sources are polar ice and ground water which account for just 2.37% of the earth's water in general. Freshwater ecosystems, though only a fraction of the total water on earth, are extremely important for the biodiversity they host and services they provide. Accounting for such a small portion of habitat globally, freshwater ecosystems support a large portion of the earth's biodiversity. There have been approximately 20,000 insect, 13,000 fish, 6,000 amphibian, 4,000 snail, 1,000 mussels, and 500 crayfish species identified as freshwater dependent. To put the scale of freshwater biodiversity into perspective, approximately one third of all vertebrate species are freshwater-dependent. Freshwater ecosystems are biologically important, and carry great importance for society as well. Drinking water, fisheries, indigenous livelihood, recreational opportunities are just some of the vast services provided by freshwater ecosystems.

Threats to freshwater ecosystems
Threats to freshwater biodiversity include overexploitation, water pollution, flow modification, destruction or degradation of habitat, invasion by exotic species, and climate change. Recent extinction trends can be attributed largely to sedimentation, stream fragmentation, chemical and organic pollutants, dams, and invasive species. Common chemical stresses on freshwater ecosystem health include acidification, eutrophication and copper and pesticide contamination. These threats can be difficult to manage due to the multilevel regulation that must be taken into consideration for conservation techniques to be successful. Unpredictable synergies with climate change greatly complicate the impacts of other stressors that threaten many marine and freshwater fishes.

Extinction of freshwater fauna
Over 123 freshwater fauna species have gone extinct in North America since 1900. Of North American freshwater species, an estimated 48.5% of mussels, 22.8% of gastropods, 32.7% of crayfishes, 25.9% of amphibians, 33% of aquatic insects, and 21.2% of fish are either endangered or threatened. Extinction rates of many species may increase severely into the next century because of invasive species, loss of keystone species, and species which are already functionally extinct (e.g., species which are not reproducing). Even using conservative estimates, freshwater fish extinction rates in North America are 877 times higher than background extinction rates (1 in 3,000,000 years). Projected extinction rates for freshwater animals are around five times greater than for land animals, and are comparable to the rates for rainforest communities. Given the dire state of freshwater biodiversity, a team of scientists and practitioners from around the globe recently drafted an emergency action plan to try and restore freshwater biodiversity.

Current freshwater biomonitoring techniques focus primarily on community structure, but some programs measure functional indicators like biochemical (or biological) oxygen demand, sediment oxygen demand, and dissolved oxygen. Macroinvertebrate community structure is commonly monitored because of diverse taxonomy, ease of collection, sensitivity to a range of stressors, and overall value to the ecosystem. Additionally, algal community structure (often using diatoms) is measured in biomonitoring programs. Algae are also taxonomically diverse, easily collected, sensitive to a range of stressors, and overall valuable to the ecosystem. Algae grow very quickly and communities may represent fast changes in environmental conditions.

In addition to community structure, responses to freshwater stressors are investigated by experimental studies that measure organism behavioral changes, altered rates of growth, reproduction or mortality. It is important to note that experimental results on single species under controlled conditions may not always reflect natural conditions and multi-species communities.

The use of reference sites is common when defining the idealized "health" of a freshwater ecosystem. Reference sites can be selected spatially by choosing sites with minimal impacts from human disturbance and influence. However, reference conditions may also be established temporally by using preserved indicators such as diatom valves, macrophyte pollen, insect chitin and fish scales can be used to determine conditions prior to large scale human disturbance. These temporal reference conditions are often easier to reconstruct in standing water than moving water because stable sediments can better preserve biological indicator materials.