Reports on experiments of underwater wet laser welding (UWLW) are scarce because of the poor forming quality of weldments. To address the key manufacturing challenges such as failure of welding with water depth exceeding 7 mm and the generation of pores and cracks which caused by the rapid water cooling, a specific self-designed flux assisted welding at different water depths (0–30 m) was innovatively proposed in this study. The microstructure, phase distribution, and properties of underwater wet laser welded duplex stainless steel joints were examined. The welding process successfully produced joints free from pores or cracks, even when performed within a 15 m water depth. In conjunction with thermodynamic calculation, the evolution process of welds and the effect of nickel from the flux on phases structure were analyzed. As the water depth increases and the welding speed decreases, the number of pores inside welds increase significantly, and no cracks are found. The penetration of all welds made in deep water is obviously smaller than that of shallow water and increased heat input does not seem to contribute to the increase of weld penetration. With the increase of water depth, a large amount of coarsened austenite consisted of columnar grains and cellular grains appear in weld zone. Texture and dislocation of the weld made in shallow water were investigated. Many dislocations including edge dislocations and dislocation entanglements arranged in austenite phase, while seldom dislocations appear in ferrite phase.