A regional chemistry transport model is used to investigate whether clouds affect tropospheric species concentrations, particularly ozone. This study focuses on boundary layer clouds in a 20¿ by 20¿ region centered over Hawaii. We find that O3 is depleted by 6% in the cloud-capped boundary layer during a 120-hour integration period. The O3 loss rate is calculated to be 320 pptv d-1 for the region, which was dominated by low NOx ( 4.5 the superoxide ion is favored, and therefore reaction of superoxide and ozone in the cloud drops increases. We discuss the importance of including transport and physical processes (e.g., deposition) on the O3 loss rate. We find that O3-rich air is transported into the marine boundary layer via subsidence and diffusion, allowing for more O3 to be depleted in an absolute sense compared to when transport and physical processes do not occur. However, the relative change in O3 is smaller in the boundary layer when transport and physical processes are included because large eddies, which are represented by vertical diffusion in the model, maintain relatively high background O3 levels in the boundary layer.