Emergent plants can not only absorb nutrients from water and sediment as a sink during the growth period, but also release nutrients such as nitrogen and phosphorus into the water environment as a source during the decline period. When the biomass is high, this release may lead to secondary pollution of the water body. To explore the nutrient release rule of typical emergent plants in Lake Hengshui and the microbial mechanism affecting plant decomposition, two dominant species Phragmites australis and Typha angustifolia, were selected as research subjects. In-situ decomposition experiments were conducted using the decomposition-bag method in Lake Hengshui at the end of February 2023. The “vertical decomposition” of plants was simulated in the experimental group which was not in contact with the water surface, and the decomposition of emergent plants was simulated in the experimental group which was flooded under the water surface. The results showed that: (1) The decomposition rates ofP. australis andT. angustifolia were significantly different under flooded and non-flooded conditions. Flooded conditions enhanced the decomposition ofP. australis andT. angustifolia, but long-term flooding might lead to the accumulation of elements. (2) The decomposition rate ofT. angustifolia was faster than that ofP. australis, because the decomposition rate was positively correlated with the initial N and P contents and the relative abundance of nitrogen and phosphorus cycling genes, and negatively correlated with the initial cellulose, lignin and soluble sugar contents. (3) The abundance of nitrogen-fixing genes increased gradually with the degree of decomposition, and the increase of N content in the litter of both species was positively correlated with the nitrogen-fixing genes of nitrogen-fixing microorganisms.