With the advancement of deep-sea exploration, the demand for underwater manipulators capable of long-duration heavy-duty operations has intensified. Water-hydraulic systems exhibit less viscosity variation with increasing depth than oil-based systems, offering better adaptability to deep-sea conditions. Using seawater as the driving medium inherently eliminates issues such as oil contamination by water, frequent maintenance limiting underwater operation time, and environmental pollution caused by oil leaks. This paper introduces a deep-sea manipulator directly driven by seawater from the deep-sea environment. To address the challenges of weak lubrication and high corrosion associated with water hydraulics, a reciprocating plunger seal was adopted, and a water-hydraulic actuator was developed. The installation positions of actuator hinges and maximum output force requirements were optimized using particle swarm optimization (PSO), effectively reducing the manipulator’s self-weight. Through kinematic and inverse kinematic analyses and joint performance tests, a six-degree-of-freedom water-hydraulic manipulator was designed with a maximum reach of 2.5 m, a lifting capacity of 5000 N, and end-effector positioning accuracy within 18 mm.