Environmental DNA metabarcoding offers an alternative approach for assessing biodiversity in freshwater ecosystems. This study applied eDNA techniques to investigate fish and mollusc communities in lake Lången, a eutrophic lake in Skövde, Sweden. The study also aims to apply eDNA metabarcoding with long-read sequencing for freshwater fish and mollusc monitoring from sediment and water samples and amplified marker genes to supplement biodiversity indications of classified fish and molluscs species for ecological management and conservation efforts of lake Lången. Samples of water and sediment were collected from four sites and were amplified using 16S and CO1 gene markers, however many samples did not manage to amplify. Sequencing conducted via Oxford Nanopore Technologies MinION was implemented for both amplified and unamplified samples and taxonomic assignment was performed using Kraken2 against custom reference databases based on local species records. Sediment samples consistently provided higher DNA concentrations and revealed greater species richness than water samples. The 16S, particularly from the MOL primer yielded the most data. Whole genome reference data enhanced classification but remained incomplete for mollusc taxon due to missing whole genome sequences. The classification findings highlight the ecological value of lake Lången among native species such as Margaritifera margaritifera, Unio pictorum, and Anguilla anguilla. As well as signalling potential invasion risks from non-native species such as Neogobius melanostomus, Dreissna polymorpha, and Sinanodonta woodiana.