Due to the vulnerability of karst hydrological systems, nitrate pollution in karst groundwater has become a global common and serious environmental problem. In order to ensure drinking water safety, it is very important to accurately identify groundwater nitrate sources. The groundwater hydrochemistry and δ15N-NO3- and δ18O-NO3- isotopes were analyzed in samples taken from a suburb of Chongqing:the Longfeng karst trough-valley, which is mainly affected by agricultural activities, and the Longche karst trough-valley, which is primarily affected by urbanization. The IsoSource model was then used to quantify the groundwater nitrate sources. The results showed that:① The NO3- concentration in groundwater ranged from 19.31 mg·L-1 to 37.01 mg·L-1(mean of 28.21 mg·L-1) in the Longfeng karst trough-valley, and from 2.15 mg·L-1 to 27.69 mg·L-1(mean of 10.31 mg·L-1) in the Longche karst trough-valley. The groundwater NO3- concentration exhibited an obvious seasonal variation in both valleys. ② The δ15N-NO3- and δ18O-NO3- isotopes in groundwater in the Longfeng karst trough-valley ranged from 3.29‰ to 11.03‰ (mean of 6.74‰) and 0.88‰ to 7.51‰ (mean of 3.18‰), respectively. In contrast, groundwater in the Longche karst trough-valley presented higher δ15N-NO3- and δ18O-NO3- values that ranged from 5.25‰ to 11.40‰ (mean of 7.95‰) and 2.90‰ to 19.94‰ (mean of 11.18‰), respectively. The lower values of δ15N-NO3- and δ18O-NO3- in groundwater in the Longfeng karst trough-valley suggest that groundwater NO3- was mainly sourced from agricultural N fertilizer, while the higher values of δ15N-NO3- and δ18O-NO3- in groundwater in the Longche karst trough-valley indicate that groundwater NO3- was primarily sourced from domestic sewage. Moreover, such δ15N-NO3- and δ18O-NO3- values in groundwater indicate that nitrification was the primary process for nitrogen conversion in both valleys. Meanwhile, significant seasonal differences in groundwater δ15N-NO3- and δ18O-NO3- were observed in both valleys; the δ15N-NO3- and δ18O-NO3- values were higher during the dry season (means of 8.83‰ and 2.79‰, respectively) than during the rainy season (means of 4.64‰ and 3.58‰, respectively) in the Longfeng karst trough-valley, whereas the δ15N-NO3- and δ18O-NO3- values were lower during the dry season (means of 9.79‰ and 14.56‰, respectively) than during the rainy season (means of 5.12‰ and 7.8‰, respectively) in the Longche trough-valley. This suggests that there were differences in the seasonal NO3- sources to groundwater in both valleys. During the rainy season, the groundwater NO3- concentration in the Longfeng karst trough-valley was mainly due to the nitrification of NH4+ in precipitation and fertilizer as well as organic nitrogen in soil, whereas during the dry season, the groundwater NO3- concentration primarily originated from domestic sewage. In contrast, the groundwater NO3- concentration in the Longche karst trough-valley primarily originated from domestic sewage in both seasons. ③ The results of the IsoSource model indicated that the nitrification of NH4+ from fertilizer and rainwater was the primary NO3- source to groundwater (44.63% of the total) in the Longfeng trough valley, and was followed by domestic sewage (29.5%), soil organic nitrogen (22.38%), and NO3- from rainwater and fertilizer (<10%). During the rainy season, the groundwater NO3- concentration was mainly due to the nitrification of NH4+ from fertilizer and rainwater (52.25% of the total) in Longfeng trough-valley, while groundwater NO3- concentration primarily originated from domestic sewage during the dry season (41% of the total). In contrast, the groundwater NO3- concentration was mainly from domestic sewage (36.17%) in Longche karst trough-valley, and was followed by the nitrification of NH4+ from fertilizer and rainwater (23.5%), soil organic nitrogen (22.5%), and NO3- from rainwater and fertilizer (<10%). The groundwater NO3- concentration in the Longche karst trough-valley primarily originated from domestic sewage in both seasons, and accounted for 47% and 25% during the rainy season and dry season, respectively.