Regional material flows are strongly influenced by human diets. To diagnose and prevent environmental problems that threaten urban sustainability, the impact of human diet changes with rapid urbanization on the regional nitrogen (N) and phosphorus (P) flows were quantitatively evaluated. A survey of day-to-day activities was conducted of 450 individuals surveyed (adults over 18 years old) in three representative areas (the central district, the new district, and the suburban/rural areas) of Shanghai, a megacity which has attracted worldwide attention. The lifestyle (eating habits, domestic sanitation, drainage facilities, etc.) pattern was determined and the potential N and P loads from human diets on the environment were calculated. The daily potential nitrogen and phosphorus loads from human diets was 19.36 g-N, 1.80 g-P in the central district, 16.48 g-N, 1.52 g-P in the new district, and 13.04 g-N, 1.20 g-P in the suburban/rural areas of Shanghai. Respondents in all three areas, especially those in the suburban/rural areas reported a preference for increasing the intake of animal-derived as well as processed foods, which means that the potential N and P load from human diets to the environment will increase further. In addition, most respondents consider industrial wastewater discharge as the main cause of eutrophication of waterbodies, though in recent years water pollution caused by domestic wastewater has increased rapidly, but this has received much less attention. Environment-friendly eating habits and improvements in the environmental awareness will be required.