The Caspian Sea is the world's largest enclosed body of water. The northern part of the Caspian sea is largely a freshwater habitat. Salinity increases gradually towards the middle part, and the southernmost part is a stable brackish ecosystem with 1.1% salinty (ca. one third of the open ocean). This bioproject contains metagenomic data from the brackish, southern region of the Caspian. A single location was sampled, at three different depths (15m, 50m and 150m). Sampling was performed at the end of summer, a time when the water column is stratified based on temperature. Briefly, 50L of water was collected from each depth and filtered serially through 20, 5 and 0.22 micron filters. These metagenomes deposited here were obtained by sequencing (Illumina HiSeq) of the 0.22 micron fraction.