The BMDV network of experts commissioned a comprehensive terrestrial biodiversity assessment of the Hamburg harbor area, enlisting local experts to conduct the surveys. This research focused on evaluating the harbor's ecological significance for both indigenous and non-native species. Surveys were conducted between 2018 and 2021. The study employed standardized methodologies for floristic mapping and habitat classification, ensuring consistency with established protocols of the Free and Hanseatic City of Hamburg and the Federal Institute of Hydrology (BfG). For this study, habitat type data from previous surveys (1983, 2005) could be mobilized, digitized and included in the analysis. Floristic mapping adhered to the city state's survey methods and metadata standards, which allowed comparisons with available data from 1975 onwards. Methodological details pertaining to the collection of zoological data are available in the accompanying publication and followed established standards for each taxonomic group (Coleoptera, Aculeata, Formicidae, Araneae, Opiliones, Culicidae). The data here contains 11008 faunistic records for the respective survey sites, recorded 2020-2021. Coordinates were recorded as centroids in ETRS89 / UTM zone 32N (EPSG 25832) and are stored in WGS84 (EPSG 4326, decimal degrees)