The ongoing research aims to improve the reliability of irrigation systems, improve methods for managing the water distribution of the operating modes of machine canals, and increase crop yields in the Nukus and Kegeyli regions of the Republic of Karakalpakstan. At present, increasing the efficiency of the operation of machine channels is associated with the development of energy and resource-saving technologies. Pumps that have been in operation for more than 25-30 years, due to physical and obsolescence, operate with low efficiency, emergencies associated with technological regimes with transients. The article analyzes changes in the processes of the hydrodynamics of control systems with optimization of sediment control on water supply structures, the danger of abrasive wear of the flow path of hydraulic units, and experimentally checks the mathematical model for managing the water distribution of operating modes. In this regard, the improvement of the design of elements and the modernization of individual units of pumping units will increase the efficiency of the entire system of machine water lifting. Recommendations are given on the inclusion of settling tanks in the composition of the head waterworks, carrying a large number of suspended sediments (more than 0.2–0.5 kg/m3) and systems for their purification.