The article deals with the operation of hydraulic structures (GTS) under the jurisdiction of the Department of land reclamation of the Ministry of agriculture of Russia, designed to provide water reclamation systems. Costs necessary for the maintenance of GTS, ensuring their operability and safe operation, carrying out repair work and other measures are considered. The study is based on information about more than 160 objects. According to the inventory of 2010–2011, the water management complex of Federal property under the jurisdiction of the Ministry of agriculture of the Russian Federation is represented by sixty thousand hydraulic structures. They include 232 reservoirs, more than 2 thousand regulating waterworks, 134 dams, 1.7 thousand supplying and pumping water from stationary pumping stations, more than 40 thousand km of water supply and discharge channels, more than 3 thousand km of protective shafts and dams and other facilities. On the basis of the study found that variation in the value of costs for operation of hydraulic structures in the various organizations 8...10 times. This is due to underfunding of operations, different service life of the GTS, their wear and tear. It is necessary to use the methodology of cost planning by types of GTS. This will ensure the normal financing of operating costs of the reclamation complex.