To investigate the operational improvements of vessels under the impact of COVID-19, this work has developed a Computational Fluid Dynamics model combined with Lagrangian particles to study the airborne transmission of COVID-19 viruses inside a ship. Initially a generic model was established to enable validation against experimental results for the diffusion of flu virus in an idealised room. Following this, the room geometry was replaced by the superstructure of a full-scale crew boat. Considering the boat advancing in open water, simulations were conducted to study the particulate flow due to a person coughing and speaking, with the boat’s forward door open and closed. The results have shown that, when the forward door is open, a significant airflow can carry the viruses to make extensive contacts with the passengers. This led to the suggestion of keeping the door closed. However, when the forward door is shut, face-to-face speaking can generate viruses that can float in the air for a long time, and it was found that the viruses mainly stay within a half-meter distance in front of the speaking person, before sinking to attach to the deck. Thus, a social-distancing suggestion on seat arrangement has been highlighted to minimise the risk of contagion. Overall, this work is expected to inform guidelines on hygienic and reconfiguring means for operators to counter COVID-19 and potentially the spread of similar viruses in the future.