Few studies have focused on the biomechanical responses of submerged, rosette-forming macrophytes to wave action, water depth, or their co-occurrence in naturally eutrophic systems. The plant architecture, root anchorage strength-related traits, leaf morphology, and biomechanics of Vallisneria natans inhabiting a range of water depths were examined along three transects (T1, T2, and T3) in a eutrophic lake, Lake Erhai, in Yunnan Province, China. These transects were exposed to weak wave action and hyper-eutrophication (T1), moderate wave action and eutrophication (T2), or strong wave action and eutrophication (T3). The results showed that V. natans was mainly distributed at intermediate depths, with the widest colonization depth in T1. The values of plant architecture, root anchorage strength-related traits, leaf morphology, and biomechanics were generally highest in T3 and smallest in T2. Along the depth gradient, these values were generally highest at 3.5, 2.5, and 2.5m for the plants growing in T1, T2, and T3, respectively. These findings suggest that V. natans adopts a tolerance strategy to cope with the effects of strong wave action in eutrophic habitats and an avoidance strategy when exposed to moderate wave action in eutrophic areas. Since the absence of an avoidance strategy increases the resistance to low-light stress at the expense of increased drag forces, there is a limit to the wave action that V. natans can withstand. This study indicates that biomechanics could be important when determining the distribution pattern of V. natans in Lake Erhai.