Litter decomposition is an important soil nutrient source that promotes vegetation in deteriorated riparian zones worldwide. The periodic submergence and sediment burial effects on two prominent annual herbaceous plants (Echinochloa crusgali and Bidens tripartite) are little known in mega-reservoir settings. Our study focuses on the mass and carbon loss and nutrient release from E. crusgali and B. tripartitle litter and changes in soil properties, which are important for riparian zone rehabilitation in the Three Gorges Dam Reservoir, China. This study adopted the litter bag method to explore the nutrient change characteristics and changes in soil properties at different sediment burial depths under flooding scenarios. Three burial depths (0 cm, 5 cm, and 10 cm) were used for these two plants, and the experiment lasted for 180 days. The results revealed that the litter decay rate was high at first in the incubation experiment, and the nutrient loss rate followed the pattern of K > P > N > C. The relationship between % C remaining and % mass remaining was nearly 1:1, and the total amount of P exhibited a leaching–enrichment–release state in the decomposition process. Nutrients were changed significantly in the soil and overlying water at the first decomposition stage. Still, the total soil nutrient change was insignificant at the end, except for the 10 cm burial of B. tripartitle. Moreover, oxidation–reduction potential was the main factor in the litter decomposition process at different burial depths. This study indicated that sediment deposition reduced litter mass loss, slowed down the release of N and P, and retained more C, but promoted the release of K. Conclusively, in litter decomposition under waterlogging, the total soil nutrient content changed little. However, litter does more to the soil than that. Therefore, it is necessary to study the residual soil litter’s continuous output after the water level declines for restoration purposes.