Submerged friction stir welding (SFSW) is a new modification of friction stir welding. In this paper, 6 mm thick 6061Al-T6 alloy plates were welded using the friction stir technique under normal air and submerged water conditions at 108 mm/min welding speeds and a rotational rate of 900 rpm. The cooling water temperature in SFSW varied at 0 °C, 35 °C, and 80 °C to clarify the effect of water temperature. The characteristic hourglass-shaped stir zone was observed in the macrostructure of all the samples. All the samples exhibited defect-free joints. The results revealed that the finer grain size of 2.43 μm was at 0 °C. The macrostructure of SFSW joints separated into the shoulder-driven zone and pin-driven zone due to the low-temperature difference between the environment and water media and the high heat absorption capacity of the water, which caused a more substantial cooling rate during water-submerged welded joints. The microhardness distribution of all the joints showed typical “W” shape characteristics. The microhardness for all submerged samples was higher than in normal air conditions due to the higher thermal cycling effect in submerged conditions. Improved dynamic recrystallization in the joint welded at 80 °C resulted in the highest tensile strength (~249 MPa) and microhardness (~95 HV).