In this study, 3990 movements of 629 different ships approaching to the Ambarlı port of Istanbul and 10,272 movements of 2798 different ships arriving at Kocaeli port which are the largest ports of Turkey were monitored for a year between September 1, 2017 and September 1, 2018. It is well known that ship exhaust emissions have a significant impact on pollutant and global warming agent mass inputs and diminish air quality around port areas. We calculated ship exhaust emissions for three different modes by ENTEC method. The annual estimated emissions were 72,802, 1430.4, 900.3, 105.3, 60.9, and 59 tons for CO2, NOx, SO2, PM10, VOC, and CO, respectively, in Ambarlı Port. Higher emissions were estimated for Kocaeli Port due to marine traffic intensity. The annual estimated emissions at Kocaeli Port were 134,120.8, 2655.1, 1652.3, 181.4, 108.3, and 106.4 tons for CO2, NOx, SO2, PM10, VOC, and CO, respectively. In order to determine the impact of ship emissions, we employed AERMOD air quality dispersion modelling. Ground-level PM10, NOx, and SO2 concentrations were calculated. Their spatial distribution was plotted and results were evaluated by air quality measurement station results. Only estimated SO2 concentrations were higher than the observed concentrations. We concluded that ENTEC calculations produce excessive SO2 concentrations. Because sulphur content of marine fuel may vary and recent amendments in the related regulations limit its amount to lower values. Advancement of on-board SO2 emission control on ships can also have a reducing effect on emitted SO2 emissions. As a result, we emphasize that current ENTEC emission factors don't represent SO2 emissions accurately. Further, the advancement of SO2 emissions factors is required.