Collecting in shallow water (water depth: ~30 m) is an emerging field that requires robotics for replacing human divers. Soft robots have several promising features (e.g., safe interaction with the environments, lightweight, etc.) for performing such tasks. In this article, we developed an underwater robotic system with a three-degree-of-freedom (3-DoF) soft manipulator for spatial delicate grasping in shallow water. First, we present the design and fabrication of the soft manipulator with an opposite-bending-and-stretching structure (OBSS). Then, we proposed a simple and efficient kinematics method for controlling the spatial location and trajectory of the soft manipulator’s end effector. The inverse kinematics of the OBSS manipulator can be solved efficiently (computation time: 8.2 ms). According to this inverse kinematics method, we demonstrated that the OBSS soft manipulator could track complex two-dimensional and three-dimensional trajectories, including star, helix, etc. Further, we performed real-time closed-loop pick-and-place experiments of the manipulator with binocular and on-hand cameras in a lab aquarium. Hydrodynamic experiments showed that the OBSS soft manipulator produced little force (less than 0.459 N) and torque (less than 0.228 N·m), which suggested its low-inertia feature during the underwater operation. Finally, we demonstrated that the underwater robotic system with the OBSS soft manipulator successfully collected seafood animals at the bottom of the natural oceanic environment. The robot successfully collected eight sea echini and one sea cucumber within 20 minutes at a water depth of around 10 m.