Countable morphological features in individuals of three mass species of fishes – roach, perch and crucian carp, living in small ponds of the Central-Eastern part of Udmurtia – were studied. The number of holes of seismosensory channels in some paired cover bones of the head skeleton of the caught fishes was counted and the sum of the values of these countable features (ΣSS) was calculated with averaging for the left and right sides. The total mineralization of water was also measured in the investigated reservoirs and the content of calcium and magnesium ions was estimated in the water. For all three fish species, one trend of interpopulation variability was revealed: with an increase of the concentration of Mg2+ in fresh water, the average value of ΣSS decreased in fish individuals from the studied populations. Statistically significant differences in mean values and frequency distributions of discrete variants of this seismosensory feature were observed for populations of roach, perch and crucian carp, living in water bodies with the greatest differences in the content of magnesium. In addition to full-scale research, laboratory experiments on aquarium cultivation of juvenile perch and roach in various hydrochemical conditions were carried out. Formed in fresh water with a high content of Mg2+, perch and roach juveniles had a smaller number of holes of seismosensory channels in some head bones in comparison with juveniles from the control groups and adult individuals of these fish species in reservoirs, where fertilized fish eggs for incubation were taken. Increased concentrations of Na+ did not have a similar effect on the formation of the studied signs. To explain the observed ontogenetic effects, we consider the possibility of direct influence of magnesium ions on the rate of larvae development of the freshwater fishes, as well as indirect influence on their morphogenesis of the competitive biochemical relations of this element with calcium.