Sound environmental management decisions - in accordance with the EU WFD for aquatic ecosystems – mainly depend on reliable species presence- and distribution- data. Here we present a workflow from sampling strategies to results and decision making using eDNA metabarcoding analyses for fish, amphibians, and mussels from habitat to landscape scales with focus on sampling strategies for "big data" in marine and freshwater ecosystems in Sweden. The project LifeDNAquatic highlights a solid eDNA pipeline and comparison of methods, which cover field planning and the entire pipeline generating data for Species Distribution Models (SDMs). Intense sampling over a large river catchment highlights previoulsy unanswered questionsand and provides insights to a priori settings for sampling strategies to retrieve "big data". The results provide novel insights to DNA distribution in the environment, seasonal and spatial changes in eDNA composition, and validation of data.