One of the major factors in an economic project of new concrete dams and safety valuation of available dams in seismic areas is the control and dissipation of the induced hydrodynamic pressure induced by dam and reservoir interaction. As one of the main control functions, dissipating the induced hydrodynamic pressure on the upstream face of the dam is considered in the evaluations. In this paper, the effects of a rubber damper as an isolation layer on the dam's seismic control have been investigated. For optimization of the rubber damper thickness and height, the Monte Carlo probabilistic analysis is used. The ANSYS program on the basis of finite element technique is applied for modeling and analysis. The Pine Flat dam in California, due to components of El Centro, San Fernando and North Ridge earthquake is modeled as a case study to evaluate the effect of upstream isolation layer on seismic control and optimization. The effect of the thickness and height of the rubber damper on reducing the responses is investigated and the optimum thickness and height are selected using sensitivity analysis for safe and economic design. The obtained results show the capability of the rubber damper in the seismic and hydrodynamic control of the sample model.