Aquatic plant restoration has become an important means of water eutrophication remediation, but the problem of producing pollution after the plant decaying has been paid extensive attentions. This study took the Phragmites australis and Typha angustifolia as the study objects, which naturally grow and widely distribute in small rivers of agricultural area at the foothills of the Fuhe River Basin, and studied the differences of decomposition and the effects on water nutrient level using the method of simulation experiments. The results showed that the residual biomass of the two aquatic plants decreased rapidly at the beginning and then decreased slowly. The decomposition rate of the P. australis and T. angustifolia were 0.0251 and 0.0169 d^-1 in spring, respectively, which are significantly higher than that in winter (0.0027 and 0.0052 d^-1). There was a certain correlation between the decomposition rate and the nitrogen and phosphorus contents and the ratio of the plants. The mineralization rate of phosphorus was significantly higher than that of nitrogen. The initial content of total nitrogen and total phosphorus in the experimental water rapidly increased in the early stage of decomposition processes, then rapidly declined in the middle period and slowly declined in the later stage. Overall, decomposition of the P. australis and T. angustifolia was greatly influenced by seasons and the initial content of nitrogen and phosphorus. The P. australis was more sensitive, and the effects of its decomposition on water quality had timeliness.