Spatial stable isotope variability (“isoscapes”) offer potential for various applications in migration ecology, wherein stable isotope values of animal tissues are compared to values measured from the environment. We used otolith oxygen (δ18O) and carbon (δ13C) stable isotope measurements to investigate seasonal movement patterns of individual Baltic Sea salmon and the migratory connectivity of one breeding population in their non-breeding areas in the Baltic Sea. Spatial variability in δ18OH2O and δ13CDIC values of the water collected around the Baltic Sea was determined to generate horizontal and vertical gridded isoscapes. Salmon individuals ascending the river to spawn were collected in early summer in four sequent years. Prior to stable isotope analysis, micro-sampling of the otolith powder was conducted using a three-dimensional micromilling system. Two selected time points from salmon otoliths, the 2nd summer in the sea and the following winter, were analysed for isotope values. The differences between summer and winter in Baltic Sea δ18OH2O values were low, whereas δ13CDIC values exhibited substantial seasonal variability. Preliminary tests of probable locations of individual salmon via spatial probability surface maps revealed that present knowledge about δ13C values is insufficient for modelling purposes. Therefore only δ18O values were used to study seasonal and annual differences in locations of individual salmon in their non-breeding areas at the sea and locations in relation to the time of ascending the spawning river. Our results indicate that during their feeding migrations salmon move considerable distances within their non-breeding area and that migratory connectivity of the breeding population varies in spatial and temporal scales, the extent of which is poorly understood in salmon ecology. We conclude that better knowledge of movements within the non-breeding areas of migratory animals is important for understanding possible drivers (e.g. resource distribution) of animal migrations. Our observations also raise concerns over how to conserve and manage populations which are continuously moving substantial distances in their non-breeding area.