[4] Original attempts to understand and monitor freshwater ecosystems were spurred on by threats to human health (for example cholera outbreaks due to sewage contamination).
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.
[17] 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.
Five broad threats to freshwater biodiversity include overexploitation, water pollution, flow modification, destruction or degradation of habitat, and invasion by exotic species.
[7] Recent extinction trends can be attributed largely to sedimentation, stream fragmentation, chemical and organic pollutants, dams, and invasive species.
[24] Common chemical stresses on freshwater ecosystem health include acidification, eutrophication and copper and pesticide contamination.
[26] The World Wide Fund for Nature's Living Planet Index noted an 83% decline in the populations of freshwater vertebrates between 1970 and 2014.
The causes of these declines are related to:[28][26] Invasive plants and animals are a major issue to freshwater ecosystems,[29] in many cases outcompeting native species and altering water conditions.
Of North American freshwater species, an estimated 48.5% of mussels, 22.8% of gastropods, 32.7% of crayfishes, 25.9% of amphibians, and 21.2% of fish are either endangered or threatened.
[6] Macroinvertebrate community structure is commonly monitored because of the diverse taxonomy, ease of collection, sensitivity to a range of stressors, and overall value to the ecosystem.
[35] In addition to community structure, responses to freshwater stressors are investigated by experimental studies that measure organism behavioural changes, altered rates of growth, reproduction or mortality.
The effects of climate change greatly complicate and frequently exacerbate the impacts of other stressors that threaten many fish,[36] invertebrates,[37] phytoplankton,[38] and other organisms.