In this paper, we analyze the removal efficiencies and characteristics of nitrogen and phosphorus in storm runoff in two ponds located in the upper and lower reaches of Xiaozhegao Stream, Lake Chaohu drainage basin. Results indicate that in the storm period, the runoff nitrogen and phosphorus levels in the upper reaches of stream are higher than those in the lower reaches. There is a good removal performance for the upper pond on both nitrogen and phosphorus (mainly in particulate), with a removal efficiency of 74% and 52%, respectively, while no evident removal performance has been found in the lower pond. During non-storm period, both ponds have good removal performances for dissolved nutrients. In the upper pond, the removal rates are 50% and 20% for nitrogen and phosphorus, respectively; in the lower pond, the rates are 72% and 16% for nitrogen and phosphorus, respectively. There is a range of nutrient concentration that ponds could play a good removal performance:if the nutrient concentration is too low, there will be no evident nutrient removal. The two ponds have different removal efficiencies on runoff nutrients due to their different locations in the catchment. The study concludes that in the upper reaches of a catchment, which is the most important area to prevent and control the loss of nutrients from storm runoff, ponds should be constructed deep and wide in the front of alluvial fan. It will enhance the physical settlement of nutrients by intercepting the runoff and lowering the flow velocity. While in the lower reaches of a catchment, it is appropriate to construct big and shallow wetlands which will remove much nitrogen and phosphorus in storm runoff by delaying nutrient retention time and promoting biological activity. The research could benefit better design of the ponds which aims to control water eutrophication.