Work was undertaken to help establish scientific evidence and provide key recommendations to inform future development of eDNA-based habitat monitoring programmes for Scotland. Samples were collected across four habitat types: marine lochs, freshwater lochs, woodland, and peatland. The survey sites were mostly situated in and around the focal study area of Loch Lomond and the Trossachs National Park (LLTNP) but eDNA sampling included other parts of Scotland such as the Cairngorms National Park. The work was carried out in a Pilot and Phase 2 stages as indicated in the ‘study_phase’ column within the Sample metadata.