Biodiversity Monitoring South Tyrol (BMS) is an ongoing survey of nature. The monitoring not only serves as basic research, but it is also intended to provide the scientific basis for political decisions concerning spatial planning, agriculture and nature conservation. Biodiversity Monitoring South Tyrol has been set up under the direction of Eurac Research in collaboration with the South Tyrol Museum of Natural History and the government of the Autonomous Province of Bolzano/Bozen. More information are available at: https://biodiversity.eurac.edu/ For monitoring running waters, a total of 120 sites spread all around the region have been identified, to be sampled within a 4-year period. After this period, the same 120 sites are sampled again, in order to build an ecological time series in the long-term. Every year 48 points are sampled:- 24 are considered as reference sites for assessing temporal variability, so this subset (with the same 24 sampling points) is sampled annually;- 24 are additional sites whose re-sampling is scheduled to happen every 4 years.For this dataset (year n. 1 of the project) stream benthic invertebrates and a set of abiotic parameters have been collected in streams and rivers of South Tyrol, during year 2021 (from March to July). Organisms were collected through a kick-net sampler (mesh size 500 µm), perturbating an area of approximately 0.05 squared metres per each subsample, closely following the protocols described by Stucki et al. (2019). Chemical analyses on water samples were performed with a portable spectrophotometer within the same day of collection (Hach Lange DR1900). Faunal nomenclature fully complies with Fauna Europaea standard (https://fauna-eu.org), whilst the operational nomenclature (column names) refers - where possible - to the list of Darwin Core terms (https://dwc.tdwg.org/list/).The dataset is available in tab-separated file format. This format can be directly imported in a spreadsheet, and converted in a .csv file if required, or in statistical computing software - if needed, refer to help/support of your specific software. As a remark, this tab-separated file contains both the metadata and the raw data.