In order to study the influences of water depth gradients on photosynthetic fluorescence characteristics of Vallisneria natans, three water depths of 0.6, 1.3 and 2.0 m were set, and Chlorophyll fluorescence characters and rapid light curves (RLCs) of V. natans grew in three water depth treatments were measured by a submersible, pulse-amplitude modulated fluorescence: Diving-PAM. The results suggested that, with water depth increasing, the number of ramets and leaves, total root length, root surface area decreased significantly, while the maximum leaf length, average leaf length, maximum leaf width did not change significantly. The growth of V. natans under 2.0 m were restricted. With the increase of water depth from 0.6 m to 2.0 m, the difference of minimum fluorescence (F₀) and maximum fluorescence (F_m) were not significant, while maximum quantum yield of photosystemⅡ(PSⅡ) and fluorescence parameter F_v/F₀ increased significantly, which indicated that photochemical efficiency of PSⅡof V. natans grew under the condition of 2.0 m was improved remarkably. The photosynthetic efficiency in leaf of V. natans grew in water depth of 2.0 m with lower light intensity was higher than that grew in water depth of 0.6 m with higher light intensity, and V. natans grew in water depth of 0.6 m had better light protection mechanisms via fluorescence quenching assay. Compared to the leaf of V. natans grew under the condition of 0.6 m, the leaf grew in water depth of 2.0 mgot higher relative electron transport rate, and the initial slope of RLCs, light suppression parameter, maximum electron transport rate and minimum saturating irradiance were significantly different. The contents of chlorophyll-a (Chl.a), chlorophyll-b (Chl.b), carotenoid (Car) of the leaf of V. natans grew in water depth of 2.0 m were significantly higher than those grew in water depth of 0.6 m, but the ratio of Chl.a and Chl.b, the ratio of Car and Chl.a were not significantly different. The experimental results above reveal that with the increase of the water depth from 0.6 m to 2.0 m, the photosynthetic capability of V. natans became weaker, however, the light protection mechanisms of the V. natans showed the reverse, indicating that V. natans was likely to adapt to different environment caused by water depths by adjusting itself photosynthetic physiology.