Friction stir welding (FSW) is classified as a solid-state joining method with no melting of the workpiece and tool. The affecting factors for creating a joint in this method are the generated heat, pressure, and large deformations in the workpiece. The generation and appropriate distribution of heat in the FSW process guarantee the creation of a high-quality and defect-free joint. One of the modifications that are used to adjust the temperature distribution to other zones of the workpiece is the usage of the Underwater Friction Stir Welding (UFSW) technique. In the present study, the FSW and UFSW processes have been numerically investigated using the indirect process simulation technique and the applied heat flux coding through the DFLUX subroutine, and the results of the temperature distribution and residual stress in the joined samples obtained using these two techniques have been compared. According to the results, it was found that the temperature distribution patterns in the FSW and UFSW processes differ significantly from each other, and these changes in the temperature distribution of the workpiece ultimately lead to a significant difference in the temperature pattern in the weld cross-section and the longitudinal and transverse residual stresses in the specimens joined by the two techniques.