Abstract <p>The introduction of pike-perch (<i>Sander lucioperca</i>) into Alakol system of lakes (southeast of the Republic of Kazakhstan) and the ongoing acclimatization measures led to the transformation of fish community and changed the pattern of food relationships between predators. The native Balkhash perch (<i>Perca schrenki</i>) in the native fish community, being an optional predator, was at the top of the food pyramid. After naturalization, pike-perch acquired a higher trophic status, and Balkhash perch began to play the role of an intermediate predator. There occurred an extension of the trophic network and the involvement of acclimatizing species in it. The increase in the numbers of pike-perch led to the “squeezing” of the Balkhash perch on freshwater Lakes Sasykkol and Koshkarkol from the pelagic zone into the tributary system. This was facilitated by the availability of nonutilized resources of the native fauna, as well as its high reproductive potential. At the same time, the biomass of the alien in freshwater lakes increased faster than the food resource was produced and utilized, whereas in Lake Alakol this was prevented by environmental factors (mineralization). In the 1990s, the numbers of pike-perch in all lakes of the system stabilized, and since the early 2000s, high fishing pressure began to restrain its growth, which allowed Balkhash perch in freshwater Lakes Sasykkol and Koshkarkol to increase their numbers and repopulate the pelagic waters of these water bodies. Regulation of pike-perch numbers opens up the possibilities of preserving the Balkhash perch as a unit of biological diversity. However, the detection of a catfish predator in the lakes of the system in 2024 may again curtail the process of restoring its numbers.</p>