In order to determine the nitrogen and phosphorus levels and sources in the subterranean river at Maocun Village in Guilin, an automatic water quality monitor was located at the outlet of the river, and sampling sites were set up simultaneously in the river basin according to the river distribution. The results show that ammonia nitrogen in 63. 4% of the samples exceeded the grade II level prescribed by the Quality Standard for Groundwater(GB/T14848—93), and total phosphorus reached the grade II level prescribed by the Quality Standard for Surface Water(GB3838—2002). There was no significant relationship between the concentrations of nitrogen and phosphorus and dry(or wet)seasons. The concentrations of total nitrogen and nitrate nitrogen gradually increased from upstream to downstream in the Maocun subterranean river basin. The total nitrogen in the Dayanqian sampling site and the subterranean river’s outlet exceeded the grade V level from the Quality Standard for Surface Water, while other indices reached the grade II level. Through comparison of real-time dynamic changes of ammonia nitrogen and total phosphorus in different rainfall conditions, it can be found that there was no visible change of the concentrations of nitrogen and phosphorus during the periods with light and moderate rain, indicating that agricultural fertilizers and domestic sewage can affect the water quality of subterranean rivers not only by means of concentrated rainfall, but also by flowing into the rivers through Karst underground pipelines. The concentration of total phosphorus reached 23. 5 μg/L, which was the instantaneeusly highest concentration during heavy rain, and ammonia nitrogen carried and diluted by rainfall was not stable due to soil erosion caused by concentrated rainfall.