Abstract: Abstract: Spatiotemporal variation of nitrate (NO3ˉ) and isotope components were investigated in the karst and non-karst sub-basins, to clarify the influence of hydrogeological conditions and underlying surface properties on the source and migration of nitrate in water. The research areas were selected as the Mudong and the Jingui sub-basin in the Qingshitan Reservoir Irrigation District of Lijiang River Basin in southwest China. Both small karst watersheds were also dominated by agricultural activity. Multiple isotopes (δD-H2O, δ18O-H2O, δ15N-NO3ˉ, and δ18O-NO3ˉ) and the Bayesian Model Stable Isotope Analysis in the R (SIAR) model were applied to compare the multiple potential nitrate sources in the water. The results indicated that the spatial and temporal variation of nitrate in water depended on the hydrogeological conditions and the associated topography, soil characteristics, and land use types of the sub-basin. Total nitrogen (TN) was mainly formed by NO3ˉ and NH4+ in the river, where the proportion of NO3￣ was slightly higher while decreasing along the river. TN was overwhelmingly dominated by NO3￣ in the shallow groundwater. Nitrification was the dominant process of NO3ˉ formation and transformation. The Jingui sub-basin included the woodland with a thicker soil layer, while the Mudong sub-basin was mainly agricultural land with the karst development and the discontinuous thin soil layer. The ranges of mean NO3ˉconcentration (0.19-15.84 mg/L), and the isotope values of δD-H2O (from -44.08‰ to -19.63‰), δ18O-H2O (from -7.24‰ to -1.55‰), δ15N-NO3ˉ (from -1.65‰ to 53.98‰), and δ18O-NO3ˉ (from 0.04‰ to 13.74‰) in the Mudong sub-basin, were all greater than those in the Jingui sub-basin. In terms of spatial distribution, the mixing of nitrogen fertilizer infiltration from the orchard of exposed karst stone mountain in the north recharge area and manure & septic waste infiltration from the village groups were not smoothly dispersed and discharged in the central tectonic basin region, resulting in the high concentration of NO3ˉ(the mean concentration range from 11.96 to 15.84 mg/L) and the high isotope value of δ15N-NO3ˉ (from 0.65‰ to 28.23‰) and δ18O-NO3ˉ (from 2.46‰ to 14.43‰) in the water of G4-G7 wells. The contributions of NO3ˉsourced from the soil nitrogen in the dry season, as well as the manure and septic waste in the wet season in the Mudong sub-basin, were less than those in the Jingui sub-basin. The reason was the low capacity of water storage in the thin soil layer that was formed by the weathering of carbonate rocks, together with the strong permeability of the shallow soil layer in the Mudong sub-basin. Consequently, spatial and temporal variations of nitrate pollution and migration in water were achieved under karst hydrogeological conditions and underlying surface properties. The finding can provide decision support for the control of agricultural non-point source pollution and the improvement of the water environment in karst and non-karst areas.