The study focuses on the microanatomy and ultrastructural changes in the trunk kidney interstitium cells and nephrons in parr, smolt, and spawning brown trout (Salmo trutta Linnaeus, 1758) sampled in Luga River and Solka River, the tributaries of the Baltic Sea. Regardless of the type of cells or their structure, there were changes in their areas and in the number and structure of organelles responsible for the transport, synthetic, and energetic functions of cells. Our data on the morphology of the nephron combined with data on its physiology suggest a fundamental change in kidney function during the parr-smolt transformation before migration; this could be a pre-adaptation for a successful life in saltwater where urine output is sharply reduced. Thus, detected structural features of the trunk kidney in S. trutta are cytological markers of the migration process. The numbers of lymphocytes, neutrophils, and eosinophils with segmented nuclei increased from parr to smolts and then to spawners; only monotypic specific granules in neutrophils were found in smolts and spawners. Cells with radially arranged vesicles were described for the first time in S. trutta renal interstitium. Their origin has not yet been established. The shape of these cells changed from spherical to trihedral during fish maturation. All the above ultrastructural changes of renal interstitium cells could be considered cytological markers of cell maturity.