The non-lethal impacts of marine vessels on cetaceans are now a globally recognised threat. This study is the first to investigate the effect of marine traffic on the behaviour of bottlenose dolphins Tursiops truncatus in the Istanbul Strait, Turkey. The Istanbul Strait (also known as the Bosphorus) is one of the busiest international waterways in the world and is exposed to dense marine traffic. The effect of marine traffic, location and season on the behavioural transitions was investigated through general log-linear analysis. Further, the changes on the behavioural budget and bout duration were assessed using Markov chains. Results showed that marine vessels were the main driving force for the behavioural transitions. These changes in transitions between behaviours led to significant changes in behavioural budget and bout durations (average time in each behavioural state). Surface-feeding, resting and socialising behaviour significantly decreased in the control budget, while diving showed an increase in the presence of vessels. Moreover, dolphins spent less time surface-feeding, resting, socialising and diving once disrupted. Furthermore, the current level of vessel-dolphin interaction (51%) in the Istanbul Strait was sufficiently high to alter the dolphins’ cumulative behavioural budget significantly. Finally, speed and distance of vessels played a considerable role in the directional responses of dolphins. These results raise concerns on the potential biological consequences of the observed behavioural changes, considering that the population is already classified ‘at risk’ and is still lacking species-specific conservation plans. The results of the study must be considered immediately to create protected zones in order to mitigate the vessel-dolphin interactions.