Conventional tags applied to individuals have been used to investigate animal movement, but these methods require tagged individuals be recaptured. Maps of regional isotopic variability known as “isoscapes” offer potential for various applications in migration research without tagging wherein isotope values of tissues are compared to environmental isotope values. In this study, we present the spatial variability in oxygen (δ18OH2O) and dissolved inorganic carbon (δ13CDIC) isotope values of Baltic Sea water. We also provide an example of how these isoscapes can reveal locations of individual animal via spatial probability surface maps, using the high-resolution salmon otolith isotope data from salmon during their sea-feeding phase in the Baltic Sea. A clear latitudinal and vertical gradient was found for both δ18OH2O and δ13CDIC values. The difference between summer and winter in the Baltic Sea δ18OH2O values was only slight, whereas δ13CDIC values exhibited substantial seasonal variability related to algal productivity. Salmon otolith δ18Ooto and δ13Coto values showed clear differences between feeding areas and seasons. Our example demonstrates that dual isotope approach offers great potential for estimating probable fish habitats once issues in model parameterization have been resolved.