The oceanographic characteristics of the Canakkale and Istanbul Straits provide interesting environments for bacteriological studies. In this study bacteriological analyses have been carried out in layers formed as a result of the salinity of the Mediterranean and Black Sea waters. Sea water samples taken from depths varying from 0-30 cm and 10-50 meters were analyzed for faecal coliform and total coliform bacteria using the Membrane Filtration Technique. Mixtures with CTD (SBE 19 SEACAT Profiles) and halocline stratifications were determined. The bacteria levels determined in water samples taken from under halocline layer in the Istanbul Strait were sometimes found to be higher in comparison to sea water samples taken from 0-30 cm. Higher bacteria levels found in the undercurrent were considered to be a result of deep discharge systems carrying domestic waste products. The indicator bacteria level determined in the Istanbul Strait were found to be higher than the sea water samples taken from the Canakkale Strait. The bacteria level in both straits showed no distinctive seasonal decrease throughout a one-year period. This shows the continuity of point and non-point sources of pollution in both regions.