<p>This study investigates the friction stir welding (FSW) of AA-6063 aluminum plates in both open-air and underwater environments. The primary aim was to estimate the distribution of spatiotemporal heat flux transients along the weld line during the joining process, using an inverse analysis method. The numerical model of the advancing side of the weld is divided into three segments along the weld line, with temperature data used as input for the inverse solver. Results indicate that the peak heat flux in segment 1 is consistently higher than in the other segments due to the initial larger temperature gradient and additional heat generated during the tool’s plunging and dwelling phases. This peak occurs earlier in segment 1 compared to segments 2 and 3. In underwater friction stir welding (UWFSW), peak heat flux values are two to three times lower than in conventional FSW. As the tool progresses along the weld&#xa0;track, heat is gradually distributed inward, with segment 3 absorbing the most heat, followed by segments 2 and 1. Moreover, the total heat absorbed by each segment during UWFSW is 3–4 times lower than in FSW, with more efficient heat dissipation into the surrounding water in the underwater process.</p>