In the process of urbanization, high-intensity human activities have seriously disturbed the river networks, especially in the core urban areas of large cities. At present, a series of urban water environmental problems, such as urban waterlogging and non-point pollution, caused by damage to the river network structure and the decrease in surface permeability conditions in high-density urban areas have received widespread attention. In this study, the effects of the river network structure and urbanization on urban waterlogging were analyzed in the Pudong New Area by using the data of waterlogging sites on the Amap. The results showed that the average water surface ratio is 10.9%, the average river network density is 4.59 km/km2, and the comprehensive impervious ratio is 42.8%. From northwest to southeast, the impervious ratio of the Pudong New Area decreases gradually, and the water surface ratio and the river density increase gradually, while the areas with high waterlogging density are mainly concentrated in the northwest districts. The correlation coefficients indicate that the river network structure (−0.710 and −0.716) has a greater impact on waterlogging than urbanization (0.608) does. The current water surface ratio (10.9%) of the study area generally meets the requirements of the suitable water surface ratio (10.0%) in a rainfall return period of 50 years. However, the water surface ratio and the river density in about half of the districts did not meet the requirements of the suitable river network structure.