The Istanbul Strait has intense maritime traffic while, at the same time, it poses significant navigational challenges. Due to these properties, there is always a high risk arising from maritime shipping in this region. Especially, substandard ships threaten life, as well as the marine environment. In this aspect, Black Sea Memorandum of Understanding (MOU) Port State Control Inspections are important for maritime safety in the Istanbul Strait, because they directly reflect the performance of ships passing through the Istanbul Strait. Stringent and effective inspections assist in the enhancement of navigation safety and help to develop sustainable environment management. In this context, this study aims to assess maritime safety for the Strait region concerning passing flag states. Firstly, to assess the performance of flag states in general, the Black Sea MOU Black-Grey-White lists were generated for the period 2004–2014 and the change in the performance of these flags was examined. Secondly, the risk level of each flag state passing from the Strait region was determined using the method of weighted points based on the Black-Grey-White List, deficiency index level, casualty index level, and passing index level.