This study aims to investigate the dissolved oxygen (DO) and total suspended solid (TSS) changes along the Gokova Bay waters. DO and TSS contents were measured in the both surface and deep waters at total 16 stations of Gokova Specially Protected Area. The highest DO concentrations were observed in the upper water in May 2006 and in the lower water in June 2006 whereas the lowest value was measured in June 2005. The highest values in the upper water were especially connected with the primary production. The reason of the higher values in the deep water was the increasing solubility of oxygen in colder water. The highest TSS contents were found in the both surface and upper part of the water column in the bay. These results suggested the terrestrial (domestic + industrial) inputs via the rivers.