This study presents the empirical analysis of residual stresses within friction stir welded 6061-T6 and 6063-T6 aluminum alloys. In the analysis, the focus lies on production parameters and thermal gradients. This further involves clamping methods, contact between the tool shoulder, and welding parameters. The investigations about the microstructures identify the nugget, TMAZ, and HAZ. Key influencing factors in this context include dynamic recrystallization, temperature gradient, and strain rates. Experiments used L9 Taguchi orthogonal array, and chemical composition was analyzed using vacuum spectrometry. Underwater friction stir welding applied pH 9 coolant for cooling. The research applied titanium diboride tools of hardness 9–9.5 Mohs in order to avoid joint defects by applying the layout of underwater welding in a wooden tank. Tensile strength ranges from 29.616 to 94.789 MPa, the maximum value indicated optimal welding conditions. Residual stresses ranged from 95 to 130 MPa, and lower stresses were preferred to minimize defects. The results indicate that optimization of welding parameters and residual stress management can significantly enhance tensile strength and structural integrity in aluminum alloys.