Surface water quality dynamics is a pivotal factor in sustainable water management. As a strategic waterway in Taihu Lake Basin (China), Taipu River plays a key role in integrating water management through flood control, water supply, and ecological preservation across Jiangsu, Zhejiang, and Shanghai. However, under evolving anthropogenic pressures, systematic studies characterizing its nutrient spatiotemporal variations and pollution drivers remain limited. In this study, the spatiotemporal (October 2020–July 2021 from upstream to downstream) distributions and source characteristics of key nutrients from Taipu River were evaluated through various water quality index methods, coupled with multi-approach source apportionment (principal component analysis and positive matrix factorization). Results indicated that the concentrations of total nitrogen (TN) and chemical oxygen demand (COD) in Taipu River gradually increased from upstream (TN: 0.9–1.2 mg L−1, COD: 11.5–15.2 mg L−1) to downstream (TN: 1.1–1.9 mg L−1, COD:11.0–21.7 mg L−1), and exceeded regulatory Class III limits in summer/winter (>1.0 mg L−1) and spring/autumn (>20 mg L−1), respectively. The increased TN likely resulted from nitrogen fertilizer loss due to rainfall, whereas the increase in COD is probably linked to the release of metabolic products from algae. Water contamination analyses identified a slightly-contaminated T7 site (i.e., TN = 1.51 ± 0.71 mg L−1, COD = 34 ± 9.0 mg L−1, exceeding Class IV), with primary contamination sources attributed to industrial activity (e.g., textile industry). For this T7 site with slight water contamination, the in-situ remediation strategies such as adding synthetic microbiomes, incorporating aquatic plants, and engineering intervention for nitrogen and COD pollution are recommended. These findings highlight the urgent requirement for targeted measures to mitigate nitrogen/COD loads, which is crucial to improve water quality and ecosystem health of the Taihu Lake Basin.
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