Motorboat noise is recognized as a major source of marine pollution, however little is known about its ecological consequences on coastal systems. We developed a State Space Model (SSM) that incorporates an explicit dependency on motorboat noise to derive its effects on the movement of resident fish that transition between two behavioural states (swimming vs. hidden). To explore the performance of our model, we carried out an experiment where free-living Serranus scriba were tracked with acoustic tags, while motorboat noise was simultaneously recorded. We fitted the generated tracking and noise data into our SSM and explored if the noise generated by motorboats passing at close range affected the movement pattern and the probability of transition between the two states using a Bayesian approach. Our results suggest high among individual variability in movement patterns and transition between states, as well as in fish response to the presence of passing motorboats. These findings suggest that the effects of motorboat noise on fish movement are complex and require the precise monitoring of large numbers of individuals. Our SSM provides a methodology to address such complexity and can be used for future investigations to study the effects of noise pollution on marine fish.