These data were generated within the framework of the Meta-IBD project, led by the Laboratoires des Pyrénées et des Landes and financially supported by the Adour Garonne Water Agency, including two scientific partners, Scimabio Interface and Artemis. The objective of the project was to compare the evaluation of diatom trophic indices obtained by the reference method (microscopy) versus the metabarcoding method, at the local scale. This comparison is based on biofilm sampling in southwest France, in the Adour, Nives and Gaves regions, in 2021 and 2022. The project ran from May 2021 to September 2023. The directory contains the following files: 756 (378 x 2 replicates) samples fastq files (file intituled MetaIBD_Biofilm2021et22_LPL.rar) - contains the 756 fastq files from the Laboratoires des Pyrénées et des Landes sequencing. Metadonnees_MetaIBD_20212022.csv - contains all the data available for each sample corresponding to the names of the sequencing fastq files.