Mixed‐stock fishery of sea trout (Salmo trutta L.) in the Baltic Sea targets wild and stocked individuals, which could lead to over‐exploitation of wild stocks. Studying the contribution of different spawning streams and hatcheries to the fishery would aid in more effective management and conservation of S. trutta. The aim of the present study was to explore whether and to what extent parr from different S. trutta spawning streams and hatcheries can be differentiated, using water chemistry and otolith microchemistry. Water chemistry samples demonstrated significant spatial variation between different study regions (Estonia and Finland); Sr, Mg, Fe, Zn, Ca and Cu contributed most to the separation. Parr collected from different sites showed a significant difference in otolith element:Ca and 87Sr:86Sr ratios on a smaller scale, including only Estonian samples (n = 361), and on a larger scale incorporating parr from Estonia, Latvia and Finland (n = 564). The reclassification rate of S. trutta parr was on average 73%, being highest in Finnish streams and hatcheries, followed by Latvia and Estonia. Otolith 87Sr:86Sr and Sr:Ca ratios were the most important in discriminating fish from different sampling sites. The present study demonstrates the potential of separating S. trutta on various spatial scales including different countries and neighbouring streams, making this the most extensive otolith microchemistry study to date in terms of streams and regions studied. The established reclassification rules form a basis for future work investigating the natal origin of adult S. trutta caught in the mixed‐stock fishery in the sea.