This data set contains fish occurrence and abundance data for 72 freshwater fish species (native and non-native) for 12 federal states (Berlin, Brandenburg, Hesse, Mecklenburg- West Pomerania, Lower Saxony, Bremen, North Rhine-Westphalia, Saarland, Saxony-Anhalt, Saxony, Schleswig-Holstein, Thuringia) in Germany, This geographic extent covers mostly middle and north Germany, including the basins of Maas, Weser, Ems, Elbe, Oder, and middle Rhine, while excluding the Danube River Basin and the upper Rhine Basin. The data set has been collected by federal authorities and experts at 12007 sampling sites for the purpose Water Framework or Habitats Directive monitoring across the aforementioned federal states: (1) Berlin; 159 sampling sites; data provided by „Fischereiamt Berlin“, (2) Brandenburg; 1179 sampling sites; data provided by „Landesamt fuer Umwelt Brandenburg, Referat W14 (Oberflaechengewaesserguete)“, (3) Bremen; 37 sampling sites; data provided by „Die Senatorin fuer Klimaschutz, Umwelt, Mobilität, Stadtentwicklung und Wohnungsbau, Contrescape 72, 28195 Bremen“, (4) Hesse; 988 sampling sites; data provided by "Hessisches Landesamt fuer Naturschutz, Umwelt und Geologie (HLNUG), Dezernat Gewaesseroekologie", (5) Mecklenburg-West Pomerania; 260 sampling sites; data provided by "Landesamt fuer Umwelt, Naturschutz und Geologie (LUNG) Mecklenburg-Vorpommern", (6) North Rhine-Westphalia; 2118 sampling sites; data provided by "fischinfo.naturschutzinformationen.nrw.de", (7) Lower Saxony; 530 sampling sites; data provided by "Niedersaechsisches Landesamt fuer Verbraucherschutz und Lebensmittelsicherheit (LAVES), Dezernat Binnenfischerei, Hannover", (8) Saarland; 63 sampling sites; data provided by "Landesamt fuer Umwelt und Arbeitsschutz Saarland, Fachbereich Gewaesseroekologie", (9) Saxony; 3735 sampling sites; data provided by "LfULG (2021): Auszug aus der Fischdatenbank SaFiDB", (10) Saxony-Anhalt; 436 sampling sites; data provided by "Landesverwaltungsamt Sachsen-Anhalt Halle (Saale) & Institut fuer Binnenfischerei Potsdam-Sacrow e.V.: Fischartenkataster des Landes Sachsen-Anhalt 1992-2021", (11) Schleswig-Holstein; 1881 sampling sites; data provided by "Landesamt fuer Landwirtschaft, Umwelt und laendliche Raeume des Landes Schleswig-Holstein", (12) Thuringia; 621 sampling sites; data provided by "Fischdatenbank Thueringen". The whole data set covers a time-span from 1985 to 2020, but the main time span, for which we know that all federal states delivered most of the available data, was 2000 to 2020. However, 6246 of the sites were only sampled once. All other sites have been sampled at least twice and one site was sampled 20 times. For each sampling event, the dataset includes information on species (latin name), number of individuals caught, sampling location (name, type (lake or river)), location (names of broader water-bodies, coordinates), sampling effort (in most cases length, but sometimes duration or area), sampling method (mostly electrofishing, but sometimes others). As most data were collected for Water Framework or Habitats Directive monitoring, it can be expected that all caught species were reported. However, the original dataset only reported detections, and not absences. Hence, here, we included zero values for all species that were not reported at a site in one year, but were present in another year at that site.

We thank all data providers for straight forward data provision and the approvals for an open source data publication! This work was carried out in a project commissioned by the German Red List Centre on behalf of the Federal Agency for Nature Conservation with funding from the Federal Ministry for the Environment, Nature Conservation, Nuclear Safety and Consumer Protection. Martin Friedrichs-Manthey was funded by the German Research Foundation DFG under the grant agreement number: 442032008 (NFDI4Biodiversity). The project is part of NFDI, the National Research Data Infrastructure Programme in Germany.