Abstract: Due to the differences in the process and extent of urbanization, large differences of non-point source pollution appeared in different regions. To study the distribution characteristics and environmental effects of urban and non-urban non-point source pollution in typical river basins, this study selected two typical hilly and mountainous areas of the Yangtze River basin (Yongchuan District, Chongqing) and plain river network area (Jintan District, Changzhou, Jiangsu) as research objects. The spatial and temporal distribution characteristics of urban and non-urban non-point source pollution in different landforms were analyzed. Combined with rainfall characteristics, the correlation between rainfall and urban and non-urban non-point source pollutants was explored. The results showed that the proportion of urban non-point source pollution was much higher than that in non-urban areas in the two regions, especially in winter (from November to March) when there is less rainfall in the hilly and mountainous area. The monthly responses of those two regions to non-point source pollutants were different. Generally, the concentrations of different forms of nitrogen and phosphorus in the hilly and mountainous area were slightly higher than those in plain river network area. In the hilly and mountainous area, the highest nitrogen and phosphorus concentrations of different forms in urban areas appeared in December, while the highest concentrations in non-urban areas appeared in August. However, the highest nitrogen and phosphorus concentrations of different forms in plain river network area appeared in November. In addition, the permanganate index of non-urban areas was higher than that of urban areas in autumn and winter. Rainfall is positively correlated with most non-urban non-point source pollutants in the two regions, indicating that rainfall is one of the main influencing factors of non-urban non-point source pollution. However, the correlation between rainfall and different non-point source pollutants can be divided into long-term response and instantaneous effect. 10-year average annual rainfall is positively correlated with most non-urban non-point source pollutants in the two regions, while rainfall during the sampling time is positively correlated with most urban non-point source pollutants in plain river network area. This study reveals the non-negligible role of urban non-point source pollution in the hilly and mountainous area and the plain river network area. Analyzing the spatial and temporal distribution characteristics and emission characteristics of non-point source pollutants from different sources is important for scientific prevention and control of non-point source pollution.