Mean value of organic matter in sediment (percent SOM) for all sampling times and sites was 2.85% (±2.16). The Lapseki station had the maximum SOM level in April 2009 (9.86%), possibly due to less variation in temperature, continuous sewage discharge, and the structure of the site, since this location is less affected by flow in the strait. The lowest SOM (0.55%) was measured at the Kilitbahir site because the highest flow in the strait is close to this site. Kilitbahir sampling site has the lowest SOM as 1.75%. During sampling period, mean SOM without taking into account of individual sampling times the maximum (5.01%) was detected at the Dardanos sampling station.