Indicator and some pathogen bacteria were investigated in both samples of Chamelea gallina and Donax trunculus collected from the northern coast of the Sea of Marmara Sea, Tekirdag, Turkey. Studies were carried out monthly from November 2005 to December 2006. The samples of C. gallina and D. trunculus which were collected from natural-growing areas by mechanical dredge implemented at approximately 5–7 m depth were examined for Staphylococcus aureus, Salmonella spp, Escherichia coli, fecal coliform and total coliform. The maximum levels (Most Probable Number: MPN) of E. coli, total coliform and fecal coliform were recorded in August in samples of C. gallina and D. trunculus. Salmonella spp. was found as positive in two samples of C. gallina and four samples of D. trunculus in the summer session. S. aureus was recorded as meanly between 12 CFU/ 100 g − 2.1 × 10² CFU/100 g in the all samples during the six months from April to October. Out of the total coliforms isolated, Citrobacter spp., Enterobacter cloaceae, Serratia marcescens, Proteus spp, non fecal E. coli, and Kebsiella pneumonia were identified as 38%, 25%, 16%, 10%, 9%, and 2% respectively. Whereas the effect of the clam types on distribution of bacteria has not been found to be statistically significant, it has been found to be significant with respect to seasonal distribution of bacteria. The highest bacteria values recorded were associated with local inputs and the increase of recreational activity in this area during the summer season.