This study describes the microbial communities of four different coastal lagoons (Laguna de Rocha, Laguna de Castillos, Laguna de Briozzo, Laguna Negra), a reservoir (Represa de India Muerta) and a sample from the South Atlantic Microbial Observatory (SAMO) in Uruguay using high throughput metagenomic sequencing with long- and short read technologies (Oxford Nanopore and Illumina). Water samples were taken from the surface or mid-water column (2 m depth for Laguna de Briozzo, 0.5 m for the other sites), at a single site or - in case of Lagoons with a salinity gradient, i.e., Laguna de Rocha, Laguna de Castillos – from 2-3 different sites with brackish and freshwater conditions, respectively. 0.1-9 L of water were prefiltered through a plankton net (20 µm) and a 5-µm filter and then filtered onto polysulfone filters with a pore size of 0.22 µm until filters were clogged. DNA was extracted from the 0.22 µm filter (small, planktonic fraction) to obtain genomic DNA of the microbial community.