We developed a 3D Eulerian-Lagrangian two-phase CFD code, which can cope with distributions of bubble radius. The simulation results were compared moderately well with those of bubbling experiments conducted in a channel for circulating stratified water. It was elucidated how the difference of the simulation conditions effects the behaviour of bubbles, dye distribution, and the intrusion of dissolved $CO_2$ into the stratification. From the results, suggested is the possibility of the code to apply to the behaviour of $CO_2$ droplets released in the deep ocean for sequestering the greenhouse gas.