Aerial surveys were conducted in the Elbe Estuary, Germany, to count harbour seals on their haul-out sites. Haul-out sites were located within the intertidal zone, usually close to the waterway or tidal creeks. The north-western border of the study area was located at river-km 728 (city of Cuxhaven) and the south-eastern border was located at river-km 632 (Mühlenberger Loch). Flights were performed monthly from August 2018 until July 2019 (12 flights in total) at low tide. Within each month, a flight date in the middle of the month was chosen, depending on the tide and weather conditions. Flights were performed with a twin-engined aircraft at a height of approximately 600 feet and at an average speed of 100 knots. The flight routes were tracked via GPS. Sighted harbour seals were photographed on their haul-out sites and the corresponding geographic position was recorded. In the office, the photos were used to count the animals. In the beginning of the pupping season in June, adult and juvenile individuals were counted separately. The sizes of individual seals were used to distinguish between both age classes. Later in the year, juvenile seals could no longer visually be distinguished from adult individuals due to the pups' rapid growth. Consequently, count data of juvenile harbour seals are only available for June 2019.