Marine traffic has both short- and long-term effects on cetacean behaviour, yet fishing vessels present a unique situation as they disturb cetaceans whilst potentially offering alternative foraging opportunities. The Istanbul Strait is a key area for the study of anthropogenic disturbance on cetaceans due to heavy human pressure in a narrow space where at least three cetacean species are regularly encountered. The present study investigated changes in behaviour of bottlenose dolphins, common dolphins and harbour porpoises in relation to the presence of purse seiners using Markov chains analysis. The results revealed increased foraging in bottlenose and common dolphins' behavioural budgets and a decrease in the time spent foraging by harbour porpoises. Moreover, a loglinear model was used to analyse the effect of possible confounding variables on observed behaviours. The only variables found to be affecting behaviour were the previous recorded behaviour, seiner presence and marine traffic density. Consequently, the presence of purse seine vessels leads bottlenose and common dolphins to change their behaviour and are related with a decrease of energy intake in porpoises. The results of this study reveal that there is an effect of purse seine vessel presence on the cetaceans found in the Istanbul Strait with potentially significant impacts on their behaviour, therefore we suggest more research is needed in the area to identify the long-term impacts of these observed behavioural changes.