Underwater friction stir welding (FSW) has been demonstrated to be a promising method for strength improvement of heat-treatable aluminum alloy joints. However, when improper welding parameters are utilized, welding defects, such as voids can be produced in the joints, leading to dramatically deteriorated mechanical properties. Thus to obtain high-quality underwater joints, it is necessary to understand the variables that promote the formation of these defects. In this study, the characteristics of welding defects in underwater joints were examined, and the formation mechanisms of the defects were investigated by analyzing the material flow patterns during underwater FSW. The results indicated that welding defects can occur at both low- and high-rotation speeds (HRS). The defects formed at HRS can be divided into two types according to the welding speed. When a HRS and a low welding speed are chosen, the material beneath the tool shoulder tends to be extruded into the pin stirred zone (PSZ) after flowing back to the advancing side. This results in a turbulent flow condition, creating void defects in the PSZ. When a high welding speed is coupled with the HRS, a large amount of material from the thermo-mechanically affected zone is dragged into the pin hole, which causes the material of the shoulder stirred zone to fill the pin hole in a downward flow direction. This leads to turbulent flow in PSZ, and creates voids or even groove defects in the as-welded joints.