In conventional design of an elevated aqueduct, apart from considering the weight of water inside the channels, hydrodynamic forces are generally neglected. In a few special cases involving high seismic zones, hydrodynamic forces have been modeled considering equivalent lumped-mass type idealization or other models. For support conditions, either the base is considered as fixed or in a few cases, equivalent spring-dashpot system is considered.However, during an intense seismic event, nonlinear soil structure interactions (SSI) may alter the response of the aqueduct significantly. This paper investigates the effect of hydrodynamic forces and SSI on seismic response of a representative elevated aqueduct model. Different modeling concepts of SSI has been adopted and the responses are compared. Frequency domain stochastic response analysis as well as time-history analysis with a series of ground motions of varying hazard levels have been performed.Demand parameters such as base shear and drift ratio are studied for varying heights of water in channels and different site conditions. From the frequency domain analysis, the effect of convective masses is found to be significant.From the time history analysis, the overall effect of increase in height of water is found to be negligible for nonlinear base case unlike the fixed and elastic base cases.For the nonlinear base condition, the base shear demand is found to decrease and the drift ratio is found to increase when compared to the results of linear base condition. The results of this study provide a better understanding of seismic behavior of an elevated aqueduct under various modeling assumptions and input excitations.