The aim of this study is to develop a seawater hydraulic piston pump for the power pack of an underwater tool system. A pump with check valves and oil–water-separated structure was selected for the purpose of improving its tolerance to particles when applied in open-circuit system. A novel ‘anti-loosening’ structure was introduced for the piston/shoe assembly. To improve the anti-wear and anti-corrosion performances of the piston and sleeve pairs under seawater lubrication, carbon fibre-reinforced polyetheretherketone was injected as an inner of the sleeve, and synthesized WC was formed on the piston with improved surface hardness. The unbalance problem of the shaft assembly was solved based on Solidworks software by adjusting the centre of mass of the shaft to its rotation axis and making all the products of inertia close to zero for an arbitrary-given coordinate system in which one of its axes is at the rotation axis. Basic performances and reliability experiments for the pump were carried out on a test rig. The shaft assembly was verified by experiment to reach very desirable balance effect. The pump has relative high efficiency at 10 MPa rated pressure and 14MPa maximum pressure. After 300 h durability test, neither excessive wear could be found for the piston/sleeve pairs as well as other parts in the pump, nor obvious performance degradation happened to the pump. The dynamic balancing method presented in this article provides an easy and effective way to solve the unbalance problem for a shaft with special structure and can be widely used in other rotating machines. New design on the seawater hydraulic pump was initially confirmed to be feasible, although further research needs to be conducted. The pump has been successfully applied in an underwater seawater hydraulic tool system.