The present report presents the results of complex long-term hydrobiological studies, the production of starter feeds (brine shrimp cysts) for aqua- and mariculture from hypersaline lakes of the Altai Territory, which includes cyst preparation during the summer-autumn period, primary cleaning of biological raw materials, activation of raw cysts and their drying. At the same time, the hatching of brine shrimp cysts is controlled, which is a key condition for obtaining high-quality starter feeds with 80–90% hatching. The factors that determine the development of brine shrimp are given and differentiated into internal and external. Critical points of the water mineralization value in hypersaline lakes for brine shrimp populations of the Altai Territory are determined as 30–340‰. On the basis of the long-term monitoring of hypersaline lakes, the zone with optimal water mineralization for brine shrimp is determined as 70–200‰. The limits of sub-pessimum and pessimum zones for the deterioration of the brine shrimp environment conditions are determined as 150–250‰ and, consequently, for the formation of their cysts. Alternation between high water level and low water level is shown on the example of hypersaline Lakes Kulundinskoye and Bolshoye Yarovoye, which determine the conditions for the development of brine shrimp and its breeding performance. The dependence of brine shrimp number and cyst number, as well as the gender structure of the population, during various hydrological periods of water level is determined. It is established that in Lake Kulundinskoye the average annual number of brine shrimps during the low water period decreases, and the number of cysts increases. The average diameter of cysts during the high water period is 230±30 μm, during the low water period it is 240±30 μm. Studies on the change in the gender structure of the shrimp population have shown that males are absent during the low water period.