Biodiversity on Earth is in rapid decline, and flowing waters are particularly affected by this. There is a long list of reasons for this starting with the impact of increased nutrient supply in the form of phosphates and nitrates from fertilizers that are washed into the water. Fine sediment such as sand from cultivated land also often moves from open soil into the rivers. When water is used for agricultural irrigation or flowing waters straightened because of land use flow velocity is reduced which can have large impact on water organisms.
In Germany for example more than 1,000 different species typically inhabit a healthy stream and despite ongoing European-wide conservation efforts, intact water bodies have become extremely rare in my home country.
Researchers from the Ruhr-Universität Bochum are investigating which environmental conditions are particularly harmful to water organisms and how to protect biodiversity in rivers and how to optimize stream restoration. Their project is called GeneStream and I believe it runs since 2013. Instead of explaining in many works what they are actually doing I let them speak as they did a nice video on the project:
The Breitenbach in Hesse is perhaps the most intensively studied stream in the world especially when it comes to its ecology and biodiversity. For more than 50 years it was the field research area for the Max Planck Institute for Limnology in Schlitz. Unfortunately, in 2006, as a result of a restructuring of Max Planck institutes, the station in Schlitz was closed but the data collected over all those decades are still used. I have been at the Breitenbach myself a few times as an undergrad and it is great to learn that this irreplaceable study site is in use again.
Two months into the experiment, the researchers analysed which organisms had settled down under different environmental conditions in the containers including some controls which were not subject to any particular environmental stress. They used DNA Barcoding to assist with the species determination. The colleagues found that all three stress factors had a negative impact on most of the species. That means that due to an increase in sediment or nutrient volume in combination with lower flow velocity the number of individuals in the test containers was significantly lower than in the control containers. An increase in sand volume had the strongest effect on the organisms. This is actually a fairly normal phenomenon but only if it happens sporadically. High sediment accumulation over years on the other hand is causing difficulties for a variety of freshwater organisms.
The GeneStream team is currently setting up a series of tests at the Felderbach stream in North Rhine-Westphalia. In this experiment, the researchers will not only identify the species present but also use population genomics to determine their genetic variation. Genetic diversity is the basis for adaptability and evolutionary 'success' of an organism. Any reasonable conservation measure should allow for gene flow between populations to counteract the detrimental effects of habitat fragmentation. You can follow the progress of the project on their website and their Youtube channel (with some funny time lapse videos).