In recent days, our AquaBOL.SK team, in close cooperation with colleagues from the Water Research Institute, has embarked on testing the practical use of barcoding data, namely metabarcoding and eDNA analysis from water, which is the first step towards the future use of molecular data in environmental monitoring of our water bodies, now based on benthic invertebrate communities. The basis is a precise sampling of environmental DNA and benthos bulk samples. The obvious part of future analyzes is also improving the barcode reference database including species that are still missing in the databases. Our first field steps have led to our major, and, in terms of cross-border cooperation, a major flow – to the Danube and Morava rivers.