Herein, the submerged friction stir welding (SFSW) technique was employed to join an AZ31C magnesium alloy (6 mm thick) using a water medium. This work investigates the influence of rotational speed, i.e., 1000, 2000, and 3000 rpm, on microstructure and tensile properties. At 1000 rpm, minor tunnel-like defects appeared due to insufficient heat input. At 2000 rpm, the welds were largely 2000 rpm yielded the highest joint quality with nearly defect-free stir zones and the best balance of strength and hardness, whereas 1000 rpm showed minor tunnel-like defects and 3000 rpm suffered from severe voids, showing optimal properties, though microscopic oxide inclusions were occasionally noted. At 3000 rpm, excessive heat and turbulent flow caused significant void defects that reduced strength and stabilized subgrain microstructure, but a further increase to 3000 rpm reduced strength due to void defects. The stir zone (SZ) expanded at higher speeds, increasing hardness to 2000 rpm, peaking at 78 HV. Fractures were observed in the thermomechanical affected zone (TMAZ) at 1000 rpm and in the heat-affected zone (HAZ) at higher speeds. Maximum tensile strength (220 MPa) happened at 2000 rpm, while void defects at 3000 rpm reduced strength. These findings provide insights into optimizing SFSW for improved mechanical properties.