This dataset contains the results of the citizen science stream monitoring project FLOW (www.flow-projekt.de), which aims to complement official freshwater monitoring programs with data on small streams. We provide data for 172 stream sites across Germany, which were monitored by over 90 trained citizen science groups in 2021, 2022 and 2023. Sampling was carried out according to protocols following the standards of the European Water Framework Directive (European Commission, 2000). For each stream site (i.e., 100m sample section), we list data on benthic invertebrate communities (sampled according to Meier et al., 2006 and identified at least to the family level). Further sampling results are listed in the related dataset (DOI). Most of the sampled streams (80%) had small catchment areas of less than 30km2 and 83 % of the stream sites were located in agricultural catchments with at least 20 % agricultural land cover (CORINE land cover class 2). 57 % of the stream sites were located in highland streams (primarily types 5, 6, and 7) and 43 % in lowland streams (primarily types 14, 18, 11, and 16).The database produced by citizen science groups was characterized by a high degree of accuracy, as results obtained by citizen scientists and professionals were highly correlated for SPEARpesticides index values (von Gönner et al., 2024). The dataset is the basis of the following publication: Julia von Gönner, Jonas Gröning, Volker Grescho, Lilian Neuer, Benjamin Gottfried, Veit G. Hänsch, Eva Molsberger-Lange, Elke Wilharm, Matthias Liess, Aletta Bonn: Citizen science shows that small agricultural streams in Germany are in a poor ecological status. Science of The Total Environment, Volume 922, 2024, 171183, ISSN 0048-9697, https://doi.org/10.1016/j.scitotenv.2024.171183.