This study serves for the definition of baseline isotopic signatures of vertebrates living in the Schlei fjord, a brackish water inlet in the north German plain, where the salinity decreases from its mouth at the Baltic Sea towards the inland locations. The Viking trade centre Haithabu and its immediate successor, the town of Schleswig, are located at opposite banks of the Schlei and constitute a settlement continuum from the 9th until the 13th century. This development not only includes a relocation of the settlement site, but also a change in economy and social structure, and witnesses the metamorphosis from an international trading locality to the rise and decline of a prototypical medieval town with town charter. In this paper, stable isotope ratios of bone collagen and bone structural carbonate of 141 vertebrate bone finds mainly of fish, birds, and sea mammals from both sites are reported to provide the baseline food web in this brackish water environment, which is the prerequisite for our ongoing studies aiming at the reconstruction of human subsistence strategies as well as the geographic origin of humans, animals, food stuffs, and raw materials in order to complete the historical picture of emerging medieval towns in a complex palaeoecosystem. In particular, we are able to show how a combination of stable isotopes from bone collagen and carbonate is capable of defining the salinity gradients in the aquatic environment.