CTD and nutrient data were collected during the ASTRA expedition aboard RV TÜBİTAK MARMARA in September 2025 in the Western Black Sea and the North-Eastern Marmara Sea. The dataset comprises vertical profiles measured from the surface down to a maximum depth of 100 m and includes temperature, salinity, density (sigma-t), dissolved oxygen (mg/L and % saturation), fluorescence, turbidity, and photosynthetically active radiation (PAR). In addition, Secchi disc depth measurements and discrete water sample analyses of phosphate (PO₄-P), total phosphorus (TP), silicate (Si), nitrate + nitrite (NOx), ammonium (NH₄-N), total nitrogen (TN), chlorophyll-a, and Winkler dissolved oxygen are provided. These data characterize the physical and biogeochemical structure of the upper water column and can support analyses of stratification, nutrient dynamics, and ecosystem processes in the study area.