Spotlight on freshwater aquatic ecosystems

24 September 2021

Freshwater aquatic ecosystems are complex and dynamic environments. They include running surface water (rivers and other waterways), wetlands (lakes, ponds, pools, but also marshes), and also groundwater. Interesting fact: freshwater covers less than 1% of the planet’s surface, but is a real reservoir of biodiversity. It is home to more than 25% of all vertebrates, more than 126,000 animal species and no fewer than 2,600 aquatic plants.

In addition to their intrinsic value as refuges for biodiversity, freshwater ecosystems provide many different services to our ecosystems, such as food supplies, flood control, water regulation and purification and CO2 storage. These dynamic environments are an integral part of the different stages of the water cycle and provide a link between land and sea environments. Yet these are the most degraded ecosystems in the world.

The general state of freshwater aquatic ecosystems

All over the world, aquatic environments are facing multiple threats that jeopardise not only how they function but also their long-term future. This deterioration is mainly due to disruption caused by humans.

The human impact on freshwater

Freshwater aquatic ecosystems are indeed significantly impacted by human activities, in particular as a result of:

  • The development and modification of waterways, altering their dynamics and leading to a reduction in biodiversity: dams, dykes, straightening, recalibration.
  • The degradation of water quality due to pollution by sediment, fertilizers, heavy metals or toxic compounds.
  • Water warming (or thermal pollution) connected to industrial wastewater emissions and agricultural drainage.
  • The proliferation of invasive alien species, such as American crayfish, American bullfrogs and water hyacinth, which can cause changes to habitats and harm to native species.

Overall, the degradation of aquatic environments is more closely connected to changes in their quality than to a decrease in their surface area. The most heavily impacted environments are wet grasslands and heaths, alluvial forests, riparian forests, bogs and marshes.

A direct threat to aquatic biodiversity

Many species need freshwater ecosystems to complete their life cycle on a permanent (fish, crustaceans, molluscs) or ad hoc (amphibians, insects) basis. In addition, wetlands provide a sanctuary for many birds, reptiles and mammals or migratory stopovers, breeding or wintering grounds for many species of aquatic birds.

Faced with the destruction, fragmentation and pollution of their natural habitat, many aquatic plant and animal species are now threatened with extinction.

The Water Framework Directive (WFD)

To address the deterioration of freshwater ecosystems, the European Union adopted the Water Framework Directive or WFD in 2000. This comprehensive legal framework aims to protect the European Union’s surface and groundwater by clearly defining different standards for ecological status.

Surface water

The main goal of the Directive is to achieve a good ecological and chemical status for all surface waters. Different quality criteria are taken into account to determine the quality of bodies of surface water:

  • Biological, such as the diversity of species and abundance of four indicator groups: diatoms, macrophytes, macroinvertebrates and fish.
  • Hydromorphological, such as flow, ecological continuity, structure of the bed and banks of the waterway etc.
  • Physicochemical, such as the abundance of nutrients, salinity, temperature or the presence of pollutants.

Combining the different criteria results in a classification system with 5 categories for ecological quality (high, good, moderate, poor and bad) and 2 categories for chemical quality (good and bad).


For groundwater, the rules are slightly different, as the Framework Directive aims to achieve a good chemical and quantitative status. The goal is to accurately measure the chemical status of the water and reduce the presence of pollutants. The following indicators are used: concentrations of nitrate, pesticides and heavy metals.

And how does Wallonia fit in with all of this?

As far as the 352 Walloon water bodies are concerned, the findings are just as striking. The general state of our surface water and groundwater is indeed not good.

Surface water in Wallonia

A slight improvement in the ecological status of surface water bodies (SWBs) has been recorded in recent years. The percentage of water bodies with a good or high status has indeed risen from 36% between 2007 and 2008 to 44% between 2013 and 2018, but the 58% target for 2021 had not yet been reached in December 2020. In contrast, the chemical status, is not improving: during the period between 2013 and 2018, the status of 68% SWBs was bad.

The main problems encountered are predominantly in the Scheldt river basin, as well as in some sub-basins of the Meuse (e.g.: Sambre, upstream and downstream Meuse, Vesdre).

Groundwater in Wallonia

As far as groundwater bodies (GWBs) are concerned, 97% had a good quantitative status and 59% a good chemical status during the period between 2014 and 2019. Nevertheless, the dry conditions recorded between 2017 and 2019 led to more water being taken from water bodies that were already regarded as being in a “poor quantitative status” and 7 of the 14 GWBs are tending to deteriorate.

It would appear that the main threats are nitrate and pesticides from agriculture, which is the primary source of pressure on our GWBs.

Using environmental DNA to monitor and protect aquatic ecosystems

Environmental DNA or eDNA is a scientific method based on looking for traces of DNA left by living organisms in their environment. Analysing water or soil samples can therefore determine the presence of plant or animal species in a given environment.

Within the context of protecting freshwater aquatic ecosystems, this method opens up some fantastic opportunities by making it possible to establish new genetic indicators of the ecological and biological status of water bodies. In particular, eDNA lets us:

– Inventory the species of fish or macro-invertebrates present in a river without having to catch them.

– Determine the species of diatoms, organisms sensitive to pollutants, quickly and with a high level of reliability.

– Establish an aquatic plant indicator without needing extensive botanical expertise.

Find out more about this useful genetic method in our dedicated article or read our articles about other topics to find out more about biodiversity.