Selection of 6 samples, with 6 Forward (R1) and 6 Reverse (R2) files, including primers. R1 and R2 reads are ca. 300 bp long, and were obtained from Illumina MiSeq technologies, at the FEM facility sequencing platform. The files refer to the18S rRNA gene reads obtained from the analyses carried out on the samples collected and filtered (SterivexTM 0.22 µm) in different areas and depths of Lake Garda on September, 2018 (see EAW_2018_FASTQ_18S_description.docx). Sampling and analyses were carried out in the framework of the project Eco-AlpsWater (ASP569), funded by the Interreg Alpine Space program. A bioinformatic protocol for analyzing these data using DADA2 is available in Zenodo: https://doi.org/10.5281/zenodo.5233527 The corresponding 16S rRNA gene reads, obtained from the same eDNA extracts, are saved in https://doi.org/10.5281/zenodo.5215815