SubBio Lab organized a workshop on groundwater biomonitoring within the COST action DNAqua-Net. The meeting attended 22 participants from nine European countries. We clarified the need for groundwater biomonitoring, in what form it could be implemented and whether molecular tools would improve its quality. We cordially thank all participants for interesting and fruitfully discussions. Special thanks go to Park Škocjanske jame that generously provided the venue for the meeting.