In the Mediterranean and other temperate waters, the stratification of the water column is a seasonal phenomenon that usually starts in April and ends in November. In this work, we have analyzed by high throughput metagenomics a fine profile of a stratified water column off the coast of Alicante, at 60 nautical miles, collected in October 2015. The bioproject contains several metagenomes and assembled genomes recovered from the same location but at different depths (15, 30, 45, 60, 75, 90, 1000 and 2000 m).