Difficulty in clarifying the deformation characteristics of deep rocks under a high water pressure environment is a technical bottleneck restricting the safe operation of large hydropower stations. In order to study the effect of reservoir water level changes on the mechanical behavior of deep limestone, a series of mechanical tests were conducted under different dynamic high water pressure environments using a self-developed hydraulic loading test device. The test results show that the unsaturated limestone always undergoes compressive deformation during the linear increase in external water pressure, and the saturated limestone changes its deformation state from compression to expansion during the linear decrease in external water pressure. The stress–strain curve of limestone shows apparent hysteresis characteristics during the cyclic increase and decrease in external water pressure. Overall, the rock strain rate showed a significant negative correlation with the external water pressure, and the rock deformation modulus showed a certain positive correlation with the external water pressure. During hydraulic loading, saturated rocks had a smaller range of variation in the strain rate and deformation modulus and were more resistant to deformation than unsaturated rocks. Limestone was subjected to both external water pressure and internal pore water pressure in a cyclic cycle, where pore water pressure promotes pore creation and expansion, while external water pressure prevents water from degrading the pore structure. The periodic change of water pressure has a significant influence on rock mechanics and deformation behavior, and the rock mass will undergo elastic deformation, plastic deformation, and even fracture. Further study of this deformation rule can provide a more accurate theoretical basis for the safe operation of water conservancy projects.