The Dardanelles (Çanakkale Strait) and Bosporus (Istanbul Strait) which have unique hydrographical characteristics were compared regarding the metabolically active bacteria, culturable heterotrophic bacteria (HPC) and their relation to the nutrients and variable environmental parameters. The samples were taken from various depths ranging from 0-30 cm to 50 meters. The halocline stratifications and mixture layer were determined with CTD (SBE 19 SEACAT Profiles). The spread plate technique was used for detecting HPC. The modified staining method was applied for identifying of the metabolically active bacteria by using epifluorescense microscope technique. The highest HPC counts were recorded to be 85±0.2x108 CFU/100 ml within the interlayer of the water column (20 m) between upper and bottom currents which were formed by the saline waters of the Mediterranean and the less saline waters of the Black Sea in the Istanbul Strait. The results show that the bacterial properties of these massive water bodies were modified by nutrient accumulation, due to the fact that terrestrial inputs with regard to chemical and biological pollution within the mixed layer. The highest metabolically active bacteria were recorded in the samples which were taken from 0-30 cm of upper layer (20-25 meters) of the Black Sea waters which enter through the Istanbul Strait. A significant positive correlation was recorded between temperature and metabolically active bacteria. The obtained results could contribute to understand variations of the bacterial activity and abundance and manage bacterial processes in a stratified water system of other marine areas of the world.