We used a FluorCam portable chlorophyll fluorescence imaging system to measure QY-max (the maximum light quantum yield, Fv/Fm, the largest light quantum efficiency of PS II) of submerged plants in wetlands of Baisha Lake and Changhu Lake, Jiangxi Nanjishan Wetland National Nature Reserve, in winter 2013. Specifically, we measured ΦPS II (PS II actual quantum efficiency), qP (photochemical quenching) and corresponding fluorescence images. Using the visual method and sampling sites method to obtain coverage, richness and abundance of submerged plants, and determined nutrient levels in water. The results show that the QY-max of Hydrilla verticillata and Vallisneria natans in Baisha Lake ranged from 0.48 to 0.68 and 0.52 to 0.71, respectively: the ΦPS II of these two species ranged from 0.32 to 0.58 and 0.20 to 0.46, respectively. The two plants had similar photosynthetic efficiency. The QY-max of Nymphoides peltatum and V. natans in Changhu Lake ranged from 0.66 to 0.77 and 0.19 to 0.68, respectively; the ΦPS II of these two species ranged from 0.26 to 0.48 and 0.22 to 0.43, respectively. The observed higher photosynthetic efficiency of N peltatum suggests it is more likely to become the dominant species. In Baisha Lake, the frequency of occurrence of plants was: H. verticillata, 90%; V. natans, 93.3%; Najas minor 26.7%, and Potamogeton franchetii 10%. In Changhu Lake, the frequency of N. peltatum was 86.7%, V. natans was 16.7%, and N. minor was 56.7%. The overall frequency of submerged plants living in Baisha Lake was much higher than that of submerged plants living in Changhu Lake, with different species dominating the two lakes. According to comprehensive analysis and comparison of trophic levels, biodiversity and photosynthetic fluorescence characteristics in the two lakes, eutrophication of Baisha Lake was higher than for Changhu Lake; and H. verticillata and V. natans were the dominant species, with similar photosynthetic activity. Conversely, in Changhu Lake, N. peltatum and V. natans were the dominant species, but the photosynthetic activity of N. peltatum was higher than V. natans. Differences in eutrophication levels in different water bodies in the Nanjishan Wetland and differing ecological niches of submerged plant species are characteristic of this system.