This study describes the microbial communities of four freshwater or brackish sites at the Baltic coast of Poland using high throughput metagenomic sequencing with long- and short read technologies (Oxford Nanopore and Illumina). Water samples were taken from the surface (0.5-1.5 m depth) of the coastal Baltic Sea in Sopot, Vistula River and two sites at Vistula Lagoon representing freshwater and brackish conditions. 0.4-7 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.