AbstractRiver ecosystems in Central Asia face significant stress from environmental changes and pollution. This study assesses temporal and spatial variations in water quality parameters within the Zarafshan River Basin using retrospective data and field measurements. Water quality indicators, including electrical conductivity (EC), total suspended solids (TSS), ammonium nitrogen (N‐NH4), nitrite nitrogen (N‐NO2), nitrate nitrogen (N‐NO3), temperature (T), chemical oxygen demand (COD), dissolved oxygen (DO), and discharge, were analyzed using the Pearson's correlation coefficient and ANOVA, with the Mann–Kendall (MK) test detecting trends over time. Obtained results indicate significant seasonal effects with elevated TSS during summer, increasing sediment load and changing aquatic habitats. The strong inverse correlation (–0.89) between DO and N‐NH4 signifies ecological challenges particularly in low DO concentrations during summer (3.25 mg L–1). Long‐term analysis identifies Navoiazot chemical factory as a major pollution hotspot. Spatial analyses based on extended sampling have revealed the Siab and Dargom canals and Samarkand City as major pollution sources of elevated N‐NO2 and COD, respectively. Trends at various gauging stations (MK‐test) show increasing EC (τ = 0.72) and N‐NH4 (τ = 0.46) levels, with decreasing TSS, N‐NO3, T, and COD levels over time. Recommendations include targeted measures to reduce pollution at the Navoiazot factory and downstream, introducing sustainable agriculture practices, increasing public awareness for environmental conservation, and improving urban wastewater treatment to meet water quality requirements for different users.