Nitrate is one of the most common pollution sources in groundwater, particularly in highly vulnerable karst aquifers. The potential for nitrification and denitrification within karst aquifers varies in different settings depending on the extent of anthropogenic inputs, so that accurate identification of nitrate sources can be difficult. Geochemical data and dual nitrate isotopes were measured in this study, incorporating a Bayesian isotopic mixing model, and used to identify nitrate sources, nitrification and denitrification, and quantitatively determine nitrate sources under different extents of anthropogenic inputs in three karst catchments within Chongqing Municipality, SW China: Laolongdong (an urbanized area), Qingmuguan (a suburban village), and Shuifang Spring (a protected natural area). At the Laolongdong catchment, the groundwater was in a reducing condition and enriched in δ15NNO3 (averaging 18.9 ± 6.9‰) and δ18ONO3 (averaging 8.5 ± 4.6‰). Manure and sewage waste were the main contributing nitrate sources. A slope of 1.8: 1 of the dual isotopes suggested a denitrification process occurring in anaerobic conduit flow. Within the Qingmuguan catchment, groundwater had average δ15NNO3 and δ18ONO3 values of 9.7 ± 3.5‰, and 1.9 ± 3.4‰, respectively. The data showed evidence for nitrification, and the contribution of soil organic nitrogen was 52.1%, followed by a contribution of 44.8% from manure and wastewater. At the Shuifang Spring catchment, the mean δ15NNO3 and δ18ONO3 values in groundwater were 8.8 ± 2.9‰, 2.3 ± 4.6‰, respectively. Nitrification was the dominant process and most of the nitrate was derived from soil organic nitrogen. This study suggests that karst underground rivers overlain by urban land use undergo denitrification, while the suburban and relatively pristine karst aquifers are dominated by nitrification, allowing development of a conceptual model for nitrate sources and transformations in karst aquifers from the categories of land use (i.e., urban, suburban, and pristine areas). Main findingAnthropogenic activities can change biogeochemical nitrogen dynamics of vulnerable karst aquifers, such that the groundwater overlain by an urban settlement has undergone denitrification, while suburban and pristine areas have been dominated by nitrification.