The article discusses the main parameters of the application of modern methods of mathematical modeling by the finite element method, necessary to assess the technical condition of low-head earth dams and identify their defects that impact the flood control system for protecting the agricultural lands of the Lower Kuban. The problem is in substantiating the necessity to extend the life of the of low-head earth dams of the flood control system in the Lower Kuban that are in unsatisfactory state and require modernization and reconstruction. The long-term operation of the low-head earth dams of the flood control system demands identification of defects and damage that violate the normal operation of the flood control system of the Lower Kuban; many structural elements fail, the soil base subsides, as well as the reinforced concrete lining can be completely destroyed. The most widespread, when assessing the residual life of the flood control system of low-head earth dams, is an integrated accident risk assessment. Based on the surveys, the technical condition of the low-pressure earthen dams of the flood control system of the Kuban River, over a considerable length, is assessed as emergency. Over a long period of operation, significant damage and changes to the main structures of the low-head earth dams of the flood control system have occurred. In many areas, the structural elements of the dams are washed up and weakened, in some areas, the ridge of the dams was found to subside by 30-50 cm, sediment accumulation in the channel in some areas led to a sharp reduction of the open cross section area with a simultaneous increase in erosion processes, etc. As a result of numerical experiments of mathematical modeling by the finite element method, the reliability of the low-head earth dams of the flood control system for various combinations of destructive influences is estimated.