Key Controlling Factors and Sources of Water Quality in Agricultural Rivers: A Study on the Water Source Area for the South-to-North Water Transfer Project

River water quality is a direct determinant of both drinking water security and regional economic vitality. However, the hydrochemical trajectories and solute provenance of agricultural streams remain only fragmentarily understood. Here, we examine the Jinqian River—a representative agricultural tributary of the Danjiangkou Reservoir source area for the South-to-North Water Diversion Project—by coupling hydrochemistry with multivariate statistics techniques. The results revealed that the pH values of the river water ranged from 7.55 to 8.30, indicating a weakly alkaline condition. During all three hydrological periods, the concentrations of total nitrogen (TN) exceeded the limits set by the Class Ⅲ surface water quality standards in China, suggesting that the agricultural river has been significantly impacted by human activities. Solute dynamics followed three rainfall-modulated patterns: (i) dilution-driven decreases in the flood season (e.g., Na+), (ii) concentration via flushing or evaporative concentration (e.g., SO42−), and (iii) reservoir-induced damping of seasonal contrasts (e.g., TN), the latter attributable to nitrogen retention behind upstream dams. Geochemical fingerprints reveal that Cl− and Na+ originate predominantly from halite dissolution; Ca2+, Mg2+ and HCO3− from coupled carbonate–silicate weathering; and SO42− from evaporite dissolution. Principal component analysis distills four dominant quality controlling factors: agricultural fertilizers, halite weathering, evaporite dissolution, and domestic effluent. These findings provide a quantitative basis for managing nutrient and salt fluxes in agricultural rivers and for safeguarding water sustainability within water-diversion source regions.