Abstract: The river network area of the southern plains of China is crisscrossed by rivers, but the slow-moving water in cut-off channels and small rivers results in a weak self-purification capacity, contributing to agricultural surface pollution. To enhance the water purification functions of ditches and rivers in the plains river network area, it is imperative to integrate their characteristics and implement collaborative management strategies of ditches-ecological ponds-disconnected beaches-small rivers tailored to local conditions. In this study, we focused on the typical ditches and rivers in the Taihu Lake Basin with the aims of investigating the spatiotemporal dynamics of N and P migration, identifying the main influencing factors, and clarifying the impact of different ditches-rivers management strategies on N and P removal rates. Through continuous in situ monitoring of N and P concentrations changes within ditches and ponds during the rice growing season, we assessed the effects of three synergistic management measures for ditches-rivers systmes: fully enclosed, semi-enclosed, and fully open. The results showed that, during the rice growing season, N and P concentrations in ditch and pond water decreased and stabilized 7 d after fertilizer application, highlighting fertilizer application as the main factor influencing these concentrations. Spatially along the water flow pathway from rice field to the entrance of the river, the different ditch-pond synergistic management measures were the key factors influencing N and P migration. Under the three management modes, the total N (TN) and total P (TP) concentrations decreased along the course of the ditch. In the fully enclosed mode, the average TN and TP removal rates were 45.15% and 55.40%, respectively. Notably, the drainage water from the fully enclosed ditch-pond was diverted to farmland after storage, minimizing the environmental risk of polluting surrounding water bodies. The semi-enclosed type demonstrated excellent purification and absorption of N and P in paddy retreat water, with average removal rates of 60.28% for TN and 74.75% for TP, considerably reducing the pollution risk to the receiving river. In contrast, the fully open mode showed lower removal rates of 22.27% for TN and 18.18% for TP, yet it still contributed to N and P removal. Overall, the synergistic management of ditches-rivers for N and P interception and purification was effective in maintaining surface water quality standards and reducing the pollution risk to the surrounding environment from paddy field drainage water.