Concern is growing about contamination of water throughout rapidly urbanizing areas in some Chinese cities. One of the most important factors is that intensive peri-urban vegetable production creates pressures to use large quantities of organic wastes and fertilizers. In order to understand the situation of N, P and K balances, a one-year field element balance monitoring in small-scale vegetable farming systems was conducted in two contrasting peri-urban areas with different industrial development in Yangtze River Delta region, China. The monitoring recorded and measured the amount and N, P and K of all inputs including chemical and organic fertilizers, irrigation water, and harvest outputs at field plot levels. N, P and K inputs were dominantly organic source in Nanjing, a vegetable-based peri-urban area, and inorganic source in Wuxi areas, an industrialized peri-urban area, while the source from irrigation water was just a little proportion (0-3%). It was found that a management (open and greenhouse management) effect (p<0.05) on total N, P and K inputs in Wuxi area, showing a significantly higher input under open field than greenhouse management. A household effect (p<0.05) in Nanjing areas was also found, depending on the off-farm income of local farmers. The more off-farm income farmers earned, the less nutrients they inputted. The site effect was also significant, which N, P and K inputs managed by migrant farmers in Wuxi area were higher than those by local farmers in Nanjing area (p<0.01), while K inputs managed by formers less than those by the latter (p<0.05). With the inputs, N, P and K outputs by vegetable harvest were significantly affected by sites (p<0.01), household in Nanjing (p<0.05), and management (p<0.01) in Wuxi, i.e. the outputs of the nutrients were significantly lower in Nanjing than Wuxi area, there were significant differences in the nutrient outputs among local farmers in Nanjing area, and their outputs under field management were markedly than those under greenhouse management. Due to application of large amounts of N and P to vegetables in two sites had caused a high positive balance of the elements in the systems and a low use efficiency of N (21.8%±4.7%) and P (20.3%±16.1%). N and P positive balance was especially high in Nanjing so that its net N increase was significantly higher than that in Wuxi area. As for K, positive balances were found in Nanjing due to heavy application of organic fertilizers (cow manure) in this area. Although the migrant farmers in Wuxi area know that K supply for cropping is necessary, but the K amount of application through chemical fertilizers didn't meet the requirement for cropping, thus, resulting in K negative balances in some plots. Surplus N and P application to vegetables, possibly associated to some extent with K deficiency, poses a serious environmental threat to water courses in peri-urban areas of the Yangtze River Delta region, China. A pronged approach, development of strategies for more efficient use of fertilizers in vegetable farming, is required to protect water quality.