<p>Nitrate pollution in source areas of interbasin water diversion projects significantly impacts drinking water safety, ecosystem health, and socio-economic development. This study focuses on the Ankang-Shiquan section of the Hanjiang River Basin, a typical water diversion source area in China. A total of 132 surface water samples were collected from the mainstream and tributaries across different hydrological seasons. The nitrate stable isotopes and Bayesian mixing model were employed to analyze nitrate transformation processes, quantify the contribution proportions of pollution sources, and assess the associated uncertainties. The results indicated that the proportion of nitrate nitrogen to total dissolved nitrogen in the water source area ranged from 41.47% to 82.74%. The nitrate concentration and stable isotopes eigenvalues showed the trend of wet season &gt; dry season, temporally. Spatially, the nitrate concentrations were higher in tributaries than in the mainstream. Nitrification was identified as the predominant process governing nitrate transformation within the water source area. Soil nitrogen, chemical fertilizers, and sewage/manure were identified as the primary sources of nitrate. The contributions of various pollution sources to nitrate were sewage/manure (41.6–59.0%) &gt; soil nitrogen (14.8–30.1%) &gt; NO₃⁻ fertilizer (9.6–16.7%) &gt; NH₄⁺ fertilizer (5.8–14.8%) &gt; atmospheric deposition (3.7–6.0%). Contributions from sewage/manure and soil nitrogen exhibited the highest uncertainties. Temporally, the uncertainties of various pollution sources were typically greater during dry season than during wet season. Spatially, the uncertainties associated with various sources in the mainstem were generally lower than those in the tributaries. The uncertainty would increase when neglecting the fractionation coefficient of nitrification.</p>