In this study, effects of three dimensional standard finite element modeling of intake tower-reservoir interaction on the linear and nonlinear seismic behavior of intake towers are discussed and results obtained are compared with the common method “Hydrodynamic added mass”. Intake tower of Doosti dam; located at Iran-Turkmenistan border; has been modeled with water of surrounding reservoir in ANSYS software, to investigate linear seismic responses due to Naghan, Tabas and Elcentro earthquakes records. Results obtained from over than 20 seismic analyses show that the seismic response of intake tower, hydrodynamic pressure distribution pattern, shear force and bending moment distribution at height and first principal stress; strongly depend on the type of modeling, type of excitation and the time of maximum top response.