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Surface water suffering from nitrate (NO3−) contamination in karst area is not only harmful to human health as drinking water but can also affect the process of carbonate rock weathering, so it is crucial to trace the sources and transformations of NO3− in karst surface water. In this study, an investigation of water chemical data and NO3− isotopes (δ15N and δ18O) was used to elucidate the transformations of NO3− and quantify a proportional apportionment of NO3− sources of individual potential sources (incl. soil organic nitrogen (SON), atmospheric precipitation (AP), manure and sewage wastes (M&S), and chemical fertilizer (CF)) in the Lijiang River (typical karst surface water), Guilin, Southwest China. δ15N-NO3− and δ18O-NO3− values of water samples from the Lijiang River range from 2.14 to 13.50‰ (mean, 6.59‰) and from − 2.44 to 6.97‰ (mean, 3.76‰), respectively. A positive correlation between Cl− and NO3− but no correlations between NO3− and δ15N-NO3− or δ18O-NO3− are found and the δ18O-NO3− values fitted the theoretical δ18O-NO3− values produced from nitrification, suggesting that the genesis of NO3− in waters of the Lijiang River is affected by nitrification processes and the mixing process has a major effect on NO3− transportation. Results of the Bayesian stable isotope mixing model show that the M&S and SON are the main NO3− source through the whole year (accounting for ~ 61% and 65% of the total NO3− in the wet and dry season, respectively), followed by CF (~ 29%). Furthermore, we find that nitrification of nitrogen in fertilizers, soil, and manure and sewage can promote the carbonate rock weathering. The estimated contribution of such nitrification to the weathering of carbonate rocks accounts for about 11% of the total carbonate rock weathering flux (calculated by HCO3−) in the Lijiang River. This finding indicates that the weathering of carbonate rock is probably affected by nitrogen nitrification processes in karst catchment. [ABSTRACT FROM AUTHOR]