This paper discusses and explains the phenomenon of salinity inversions in the thermocline offshore from an upwelling region during upwelling favorable winds. Using the nontidal central Baltic Sea as an easily accessible natural laboratory, high-resolution transect and station observations in the upper layers are analyzed. The data show local salinity minima in the strongly stratified seasonal thermocline during summer conditions under the influence of upwelling favorable wind. A simple analytical box model using parameters (including variation by means of a Monte Carlo method) estimated from a hindcast model for the Baltic Sea is constructed to explain the observations. As a result, upwelled water with high salinity and low temperature is warmed up due to downward surface heat fluxes while it is transported offshore by the Ekman transport. The warming of upwelled surface water allows maintenance of stable stratification despite the destabilizing salinity stratification, such that local salinity minima in the thermocline can be generated. Inspection of published observations from the Benguela, Peruvian, and eastern tropical North Atlantic upwelling systems shows that also there salinity inversions occur in the thermocline, but in these cases thermocline salinity shows local maxima, since upwelled water has a lower salinity than the surface water. It is hypothesized that thermocline salinity inversions should generally occur offshore from upwelling regions whenever winds are steady enough and surface warming is sufficiently strong.