The fluctuation of most of the hydrograph in the deep aqueous system records the fluid pulsation in lithosphere and variation of the earth's crust. Many observations have verified that groundwater is an ideal information carrier of the crust. In this paper, the series of input (precipitation, air pressure, Earth tide etc.) and output (water level, artesian flow) of the deep aqueous system are studied by using the spectrum analysis and system theory. The application concepts of transfer function and the spectral structure of the hydrograph enrich the knowledge of the deep aqueous system. Two typical spectral structures of the hydrograph of the deep aqueous system are obtained by comparing with many water-bearing systems of the Jizhong depression. One is from well Ma-17 and the other is from the well Xinze-5. Finally, the physical models of forming the spectrum of the hydrograph are constructed on the basis of the spectrum research on the deep aqueous system.