To assess nitrogen and phosphorus pollution in rivers of Shanghai, this study explored 65 water samples from 11 rivers in 19 districts of Shanghai from July 2012 to July 2013. The results showed that Shanghai rivers display incomplete tidal and river network characteristics under the effect of tide and rainfall, which caused temporal distribution differences of nitrogen and phosphorus pollutants. This combination of factors also affected the biodegradation in the rivers. Rainfall and tide had a diluting effect in the rivers during the experiment. There was a significant difference between the rivers of Shanghai in the nitrogen and phosphorus concentrations (P<0.05). In general, the difference appeared in a ring-like form on the map of the river network, with suburban rivers having lower concentrations of nitrogen and phosphorus than the urban rivers. Rivers located in southern sections of the Huangpu River have better water quality compared to the northern parts, and the concentration of nitrogen and phosphorus in rivers near the Jiangsu Province (northwest of Shanghai, near the estuary of the Yangtze River) were higher than in the sections near the Zhejiang Province (southeast of Shanghai) (P<0.05). Such distribution of pollutants reflected the close relationship between the concentration of pollutants and urbanization level. Cluster analysis (CA) did not find a significant difference in pollutants between the rivers of Shanghai, whereas multidimensional scaling, opposite to the CA, supported the results of the water quality assessment. Water quality of rivers after ecological restoration improves compared to the state before or to the rivers without ecological restoration (P<0.05), indicating that ecological restitution has potential in improving the water quality of rivers.