Harbour porpoises are the most common small cetaceans in the North Sea and Dutch coastal waters. To study their trophic level and feeding location, stable carbon and nitrogen isotope ratios (δ13C and δ15N) were analysed in muscle and bone samples collected from 157 porpoises stranded along the Dutch coast (2006–2008). In addition, samples from 30 prey species were analysed. Prey samples showed high δ15N values in species of higher trophic level. In addition, geographic differences in isotopic composition were found, with higher δ15N and δ13C values in prey from more southern, coastal and estuarine areas. Based on muscle δ15N values, we found neonatal enrichment and that larger porpoises, in particular males, seem to feed on lower trophic level species, compared to smaller individuals. Also bone δ15N values show that larger animals had fed on lower trophic levels in distant times. Porpoises from the Eastern Scheldt reveal distinct δ13C values in muscle, but not in bone. This shows that these animals had foraged in the Eastern Scheldt for a longer time period but were not born there. Seasonal variation in bone δ15N and δ13C values revealed two distinct groups of porpoises along the Dutch coast, a winter group (mainly males) that migrated from neighbouring regions and a Dutch subpopulation in summer. These results furthered our insight about shifts in trophic level and feeding location of harbour porpoises from the southern North Sea over time.