Despite their global distribution and ecological importance, little information about microbial diversity is available from small, shallow and ephemeral freshwater systems. A previous study over a monthly two-year survey allowed to discover a wide diversity of microorganims in the ecosystems, as well as strong temporal patterns.</p><p>The goal of this project is to monitor seasonaly the same ecosystems, and compare the eukaryotic and prokaryotic diversity in one brook and four shallow ponds located in the "Natural Regional Park of the Chevreuse Valley", France during 8 years (October 2011-January 2019). The study is based on the identification and comparison and time tracking of operational taxonomic units (OTUs) infered from Illumina MiSeq amplified 18S and 16S rRNA gene fragments of eukaryotes and prokaryotes in the 0.2-30 micrometer-size range.