Nitrate pollution in groundwater has become a common environmental problem. From April to October in 2017, four sampling sites (a hotel's tap water, septic system, Sinkhole 1^# and Shuifang spring) in Jinfoshan Karst, Chongqing were monitored every 24 days to investigate the sources and transformations of nitrate. The hydrochemistry and δ¹⁵N_nitrate, δ¹⁸O_nitrate isotopic analyses were carried out. The sewage from hotel was degraded in the septic system, then discharged into the subterranean river by the Sinkhole 1^#, and finally drained at Shuifang spring. Results showed that the concentrations of nitrate ranged from 4.65 to 10.20 mg/L at Shuifang spring, which was at a low level comparing with the standard of drinking water in China. The three high-value periods of the electrical conductivity and concentrations of nitrate and chloride at septic system, Sinkhole 1^# and Shuifang spring corresponded well to the increase in the number of tourists. The isotopic nitrate compositions of hotel's tap water were found to range from 3.7‰ to 5.8‰ for δ¹⁵N_nitrate and from 1.6‰ to 2.7‰ for δ¹⁸O_nitrate, indicating that the nitrate mainly originated from soil organic nitrogen maintaining at a natural background value. The δ¹⁵N_nitrate and δ¹⁸O_nitrate at Sinkhole 1^# varied from 14.4‰ to 21.1‰, and from 3.5‰ to 11.2‰, respectively, revealing that manure & sewage was the main source of nitrate at Sinkhole 1^#. The δ¹⁵N_nitrate and δ¹⁸O_nitrate at septic system and Shuifang spring varied between 3.7‰ and 17‰ for δ¹⁵N_nitrate value, and -9.0‰ and 7.3‰ for δ¹⁸O_nitrate value, suggesting that soil organic nitrogen and manure & sewage were the major sources of nitrate which was dominantly derived from the domestic sewage of the hotel. In hotel's tap water and groundwater from Shuifang spring, assimilation is the main process of nitrate transformation. While effluent in septic system, one of the important sources of nitrate in the subterranean river system was affected by nitrification. The wastewater at Sinkhole 1^# was characterized by denitrification. A SIAR model was used to estimate the contribution of each nitrate source to total nitrate at Shuifang spring, which indicated that the contribution rate of atmospheric precipitation, soil organic nitrogen and manure & sewage were roughly 28%, 36% and 36%, respectively.