The dataset consists of information on fish abundance (qPCR data) and diversity (HTS metabarcoding) measured through environmental DNA (eDNA) sampling. eDNA samples were collected from the Acqua Alta oceanographic platform, located in the northern Adriatic Sea, 5 nm outside of the Venice lagoon. Samples were collected over 4 weeks, from the 22nd of May 2023 to the 17th of June 2023. eDNA samples were aquired using both active and passive methods (i.e. filtration and passive filter deployment). DNA was extracted using a commercial kit (DNEasy Blood & Tissue) and quantified using a universal qPCR assay targeting fish (MiFish-U primers). Metabarcoding will be performed with Oxford Nanopore Sequencing using markers targeting 12S and COI genes. This data will provide information regarding the abundance and diversity of the fish communities, as well as produce methodological advice regarding active/passive sampling methods. The sampling campaign was carried out entirely in collaboraton with ISMAR Venice, but most of the lab work and data analysis is/will be carried out at Atlantic Technological University (Ireland) by the PI of the project (Maddalena Tibone). The sample collection metadata and qPCR analysis data is already available, while the metabarcoding data will be made available as soon as sequencing is performed.