Most anthropogenic influences on marine ecosystems, except for river- or terrestrial-borne pollution, involve some sort of vessel activity. Increasing anthropogenic activities mean that many countries are being forced to develop spatial planning schemes, while at the same time implementing conservation sites for sensitive species at sea. The effects of ship traffic on seabirds sensitive to human disturbance are currently too poorly understood to allow for the development of proper planning and conservation guidelines. We therefore used aerial surveys and experimental disturbance to elucidate the effects of passing ships on the distribution patterns, habitat loss, and species-specific flight reactions of birds, as well as the potential for habituation. Loons (Gavia spp.) showed clear avoidance of areas with high shipping intensity. Flush distances of four sea duck species differed significantly, with the longest distances recorded for Common Scoters (Melanitta nigra) and the shortest for Common Eiders (Somateria mollissima). Flush distance was positively related to flock size. Among all the sea duck species studied, the duration of temporary habitat loss was longest for Common Scoters. We found indications of habituation in sea ducks within areas of channeled traffic. However, it is questionable if habituation to free-ranging ships is likely to occur, because of their unpredictable nature. We therefore recommend that spatial planning should aim to channel ship traffic wherever possible to avoid further habitat fragmentation and to allow for habituation, at least in some species. Information on the effects of shipping on other seabird species and during different periods of the year is urgently needed, together with information on the effects of different types of boats, including recreational and fishing vessels.