Enclosed areas such as embayments with high levels of marine traffic may put at co-occurring cetaceans at risk due to collisions with vessels. The distribution of seven cetacean species and their spatial overlap with navigation routes of large cargo ships, fishing vessels and recreational vessels were evaluated off the major port in Mejillones Bay, northern Chile. Shipping distribution, navigation speeds and cetacean positions were obtained from land-based theodolite surveys. Sighting positions were also recorded from boat-based surveys. Overlap analysis based on 50% Kernel density estimations suggested that the spatial distribution of fin and humpback whales overlapped with a high concentration of large cargo vessel navigation paths. These results point to the need for the implementation effective regulation of vessel speed to mitigate the risk of collision in Mejillones Bay.