Dynamic response analysis is carried out for an aqueduct structure of the South-to-North Water Transfer Project. The interaction of water and aqueduct wall is simplified using Housner method. Six different water depths (empty aqueduct, 1/4 water depth, 1/2 water depth, 3/4 water depth, designed water depth and full water depth) are considered and calculation is conducted using time-history analysis method. The variation rule of dynamic stress and dynamic displacement are gained under different water depths. Results show that water has great influence on aqueduct body and its dynamic response. Dynamic displacement and dynamic stress of the aqueduct structure increase with the aqueduct water level increases. When water depth is bigger, dynamic displacement response and dynamic stress response are later than corresponding earthquake excitation. The relative stiffness of the longitudinal beam and the transverse beam should be fully considered in order to reduce stress concentration of aqueduct body.