Data on the occurrence of harbour porpoises (Phocoena phocoena) in German waters from 1988 to 2002 were collected from dedicated aerial surveys, incidental sightings and strandings. Aerial surveys conducted in 1995 and 1996 revealed a mean abundance of 4288 (in 1995) and 7356 harbour porpoises (in 1996) in the German North Sea study area. Mean abundances of harbour porpoises in the German Baltic Sea, divided into two subunits (blocks B and C), were estimated at 980 and 1830 (in 1995 and 1996 resp.) and at 601 (in 1995; there were no sightings in block C during the 1996 survey). From 1988 to 2002, 791 incidental sightings of harbour porpoise pods were reported in German and partly Danish coastal waters of the North and Baltic Seas. In the period 1990 to 2001, 996 harbour porpoises were found stranded along the German North Sea coast and 17 animals were identified as by-catch. In the same period 229 harbour porpoises were found stranded along the German Baltic Sea coast and 105 animals were incidentally taken in fisheries. The proportion of by-caught harbour porpoises was significantly larger in the Baltic Sea. Different monitoring methods are helpful for different aims and management issues: aerial surveys cover large areas in a short time and provide information on density, abundance, distributional patterns and seasonality. Incidental sighting and stranding networks provide indications of general distribution, seasonal variation in abundance, age distribution, by-catch and of areas which are important in the harbour porpoise’s life cycle. Comparison of data from the North and Baltic Seas revealed a higher abundance of harbour porpoises in the North Sea than in the Baltic Sea. Altogether the data sets demonstrated a strong seasonality of harbour porpoise occurrence off the German coast with highest numbers during the summer months. Important habitats for harbour porpoises were detected west of the islands of Sylt and Amrum in the North Sea and around the Schlei estuary, in waters west of Fehmarn and the Fischland-Darss area in the Baltic Sea.