The seasonal distribution of harbour porpoises in the German North Sea was investigated, hot spot areas were identified and the proportion of porpoises potentially affected by the imminent construction of offshore wind farms was estimated. Data were collected during dedicated aerial surveys conducted year-round between 2002 and 2006 following line transect methodology. Survey effort amounted to 44739 km during which a total of 5121 harbour porpoises was detected, including 258 calves. Our data suggest that porpoises move to distinct areas on a seasonal basis as their biological requirements change. They move into German waters in early spring, reach high numbers in early summer and move out of the area in autumn. The abundance estimates for the German exclusive economic zone and 12 n mile zone were highest in spring (55048 animals; 95% CI: 32395 to 101671) and summer (49687 animals; 95% CI: 29009 to 96385) and lowest in autumn with 15394 animals (95% CI: 8906 to 29470). Important aggregation zones were detected in offshore waters: in spring, 2 hot spots, Borkum Reef Ground and Sylt Outer Reef (SOR), were identified as key foraging areas. In summer, only the large hot spot SOR persisted, causing a strong north–south density gradient. In autumn, porpoises were more evenly distributed. Most mother-calf pairs were observed during spring and summer in the SOR, underlining its importance as a foraging area when reproductive costs are high. Spatial overlap exists between important areas for porpoises and areas where offshore wind farms are currently licensed or planned. The proportion of the national stock possibly exposed to the construction noise of 18 licensed wind farms was estimated applying different scenarios. Within a 20 km zone of responsiveness—as worst case scenario—39% of the harbour porpoise stock in the German EEZ could be affected during construction.