The Water Framework Directive (WFD 2000/60/EC) is the European umbrella for the assessment and regulation of ecological quality of water systems (lakes, rivers, transitional waters, coastal waters). The scope of WFD is to improve the ecological status of the aquatic ecosystems. To do so, a long time-series of monitoring campaigns within WFD exists with the ultimate goal to protect coastal ecosystems from degradation. Further, WFD project employs the calculation and improvement of ecological quality indices for the definition and assessment of eutrophication. In the submitted sub-project within WFD, the viral metagenome of 15 samples collected in 2014 and 2015 is sequenced and analyzed for several genes for the study of taxonomy and potential function of double-stranded DNA viruses.