Based on the observation of a complete hydrological year from June 2014 to May 2015, the temporal and spatial variations of the main inorganic nitrogen (MIN, referring to NO3--N, NO2--N, NH4+-N) in surface water and groundwater of the Li River and the Yuan River wetland succession zones are analyzed. The Li River and the Yuan River are located in agricultural and non-agricultural areas, and this study focus on the influence of surface water level and groundwater depth and precipitation on nitrogen pollution. The results show that NO3--N in surface water accounts for 70%-90% of MIN, but it does not exceed the limit of national drinking water surface water standard. Groundwater is seriously polluted by NH4+-N. Based on the groundwater quality standard of NH4+-N, the groundwater quality in the Li River exceeds Class III water standard throughout the year, and the exceeding months’ proportion of Yuan River reaches 58.3%. Compared with the Yuan River, MIN in groundwater of the Li River shows significant temporal and spatial variations owing to the influence of agricultural fertilization. The correlation between the concentrations of MIN and surface water level is poor, while the fitting effect of quadratic correlation between NH4+-N concentration and groundwater depth is the best (R2=0.9384), NO3--N is the next (R2=0.5128), NO2--N is the worst (R2=0.2798). The equation of meteoric water line is δD =7.83δ18O+12.21, indicating that both surface water and groundwater come from atmospheric precipitation. Surface infiltration is the main cause of groundwater NH4+-N pollution. Rainfall infiltration in non-fertilization seasons reduces groundwater nitrogen pollution, while rainfall leaching farming and fertilization aggravate groundwater nitrogen pollution.