Spatial and temporal changes in bacterial and cyanobacterial abundances were studied at three stations in monthly intervals over a period of one year in the Cilician basin shelf waters. Both populations displayed an apparent decrease in abundance with depth except winter during which a homogeneous distribution was achieved due to convectional mixing. Annual average bacterial and cyanobacterial biomass yield of the nearshore shelf station exceeded 1.8, 2.7 and 2.3, 5.4 fold of the middle and offshore stations, respectively. Both populations have been found most abundant during summer and least during winter in the entire shelf. Based on seasonal water column averages of both abundance and biomass, summer was followed by autumn, spring and winter in decreasing order. Cyanobacteria Synechococcus spp. was found more abundant at or near surface waters with elevated temperatures during the summer. In general, bacterial biomass exceeded the cyanobacterial biomass in the water column throughout the year. Cyanobacterial abundance and biomass have positively correlated with bacterial abundance and biomass, water temperature, photosynthetic active radiation (PAR), particulate organic carbon (POC) and particulate organic nitrogen (PON), and negatively with depth, density, in-situ fluorescence, nitrate and dissolved oxygen (DO) at midshelf. Similarly, bacterial numbers and biomass have displayed significant positive correlations with water temperature, cyanobacterial abundance and biomass, particulate organic carbon (POC), particulate organic nitrogen (PON) and photosynthetic active radiation (PAR), and negative correlation with depth, density, dissolved oxygen (DO) and nitrate in the offshore station.