Current analysis emphasizes on microstructural, mechanical, and corrosion behaviour of friction stir welding (FSW) joints of AA6061-T6 Al alloy and AZ31B Mg alloy using various cooling mechanisms i.e., air cooling, forced water cooling, and underwater cooling. The air-cooled, forced-water cooled, and underwater cooled FSW are abbreviated as Air-FSW, FCFSW, and UWFSW respectively. The X-ray diffraction (XRD), scanning electron microscopy (SEM) and energy dispersive X-ray (EDS) analysis established the formation of intermetallic compounds (IMCs) layers of varying thickness with composition of Al12Mg17 and Al3Mg2 at the bonding interaction of the joints. The surface appearance of Air-FSW joints was observed rougher and darker due to generation of more heat while the appearance of surface of UWFSW joints was smoother and brighter because the generated frictional heat was taken away by the water. Due to reduction of the heat and so the temperature in FCFSW and UWFSW joints, the development of IMCs got reduced, resulting in improved weld strength and joint efficiency. Occurrence of weld crack in the weld stir region was reduced in FCFSW joint as compared to Air-FSW joint. Whereas, very few or no cracks were observed in weld stir region of UWFSW joints. Maximum joint's strength of Air-FSW joints was observed 120.74 MPa, which increased to 151.56 MPa and 182.7 MPa with FCFSW and UWFSW respectively. Air-FSW joint exhibited a brittle fracture mode but in water medium, their fracture path was shifted to ductile mode which demonstrated the formation of enhanced ductility of the UWFSW joints. The corrosion resistance got improved when the joints were prepared in underwater medium.