The data concern nutrient concentrations in the water column from five selected stations in the Cretan Sea and the southeastern Ionian Sea. The samples were collected during the oceanographic cruise that took place in April 2025 within the framework of the CLIMPACT project. Water samples were collected using the rosette sampling system aboard the R/V AEGAEO, at discrete depths throughout the water column, from the surface to the seabed at each station. Depending on the maximum depth of each station, samples were collected from 12 to 18 discrete depths. The...