Simple SummaryThis article presents new data on the histology and ultrastructure of the trunk kidney in two isolated populations of Atlantic salmon, from the Baltic and Barents Seas, covering both the freshwater and the seawater period of their life cycle. We studied juvenile salmon living in freshwater (parr), juvenile salmon running into the sea (smolts), adults feeding in the sea, adults returning to their natal river to spawn, and spawning individuals. According to the results obtained, the ultrastructural changes in the nephron, believed to affect the glomerular filtration rate and the amount of urine produced in salmon kidneys, occurred as early as the smolting stage. Such alterations reflect fundamental changes in the course of pre-adaptation to life in salt water. In the Barents Sea population, the adult salmon caught in the sea had the most pronounced ultrastructural changes, which are characteristic of marine fish. In the salmon that entered the river mouth and stayed in the fresh water for less than a day, structural rearrangements occurred only in the distal tubules of the nephron. The salmon from the Baltic Sea population had less pronounced differences in the morphometric characteristics of the nephron among the studied ontogenetic stages, apparently because of the low salinity in the sampling area. In both studied populations, the activation of cellular immunity was initiated during the parr–smolt transformation. Another distinct immune response was registered in the adults returning to the river for spawning.AbstractThis article presents data on the mesonephros histology and ultrastructure in the Atlantic salmon from the Baltic Sea and Barents Sea populations, with an emphasis on comparisons between the following ontogenetic stages: parr, smolting, adult life at sea, the adults’ return to their natal river to spawn, and spawning. The ultrastructural changes in the renal corpuscle and cells of the proximal tubules of the nephron occurred as early as the smolting stage. Such changes reflect fundamental alterations during the pre-adaptation to life in saltwater. In the Barents Sea population, the adult salmon sampled in the sea had the smallest diameters of the renal corpuscle and proximal and distal tubules, the most narrow urinary space, and the thickest basement membrane. In the group of salmon that entered the mouth of the river and spent less than 24 h in freshwater, the structural rearrangements occurred only in the distal tubules. Better development of the smooth endoplasmic reticulum and a greater abundance of mitochondria in the tubule cells were observed in the adult salmon from the Barents Sea compared to those from the Baltic Sea. Cell-immunity activation was initiated during the parr–smolt transformation. Another pronounced innate-immunity response was registered in the adults returning to the river to spawn.