China has one of the largest areas of agriculture and one of the highest application rates of chemical fertilizer in the world. Agricultural non-point source pollution has became important source of nitrogen (N) pollution of surface water. In this study, the delta N-15 and delta O-18 isotopes of nitrate as a tool were used to reveal the sources of nitrate in water bodies in the Nala watershed, at a sugarcane planted area in Guangxi, China. According to the analyses based on a stable isotope analysis in R (SIAR), the mean contributions of different nitrate sources in the Nala watershed could be ranked as follows: manure (39.90 %) > soil N (SN) (34.94 %) > chemical fertilizer (CF) (17.77 %) > rainfall (7.39 %) in July; manure (42.30 %) > SN (33.54 %) > CF (24.16 %) in December. The CF and SN collectively mean contributing > 50 % of nitrate both in July and in December in the watershed, therefore, reducing the use of CF is the key to control nitrate pollution in the Nala watershed. Manure also composed a substantial contribution (mean 39.68 %, in July and December) to nitrate in the small watershed, it is necessary to provide recycle treatment for manure for the purpose of alleviating the pollution. The delta N-15 and delta O-18 isotopes of nitrate can accurately identify various sources of nitrate and SIAR offers a useful method to quantify the contribution rates of different N sources to the N pollution of watersheds.