<p>This study explores the spatial and temporal variations and driving factors of surface water quality of tidal river network areas in estuarine megacity, using the Huangpu River Basin in the Yangtze River Delta as a case study of Shanghai. A comprehensive Water Quality Index (WQI) approach, combined with Mann–Kendall test, correlation analysis, redundancy analysis, and geographic information system tools, was used to assess water quality trends in this study. From 2014 to 2023, significant improvement in water quality was observed, with conditions during the non-flood season generally superior to those during the flood season. From upstream to downstream, water quality initially deteriorated and then improved before 2021, but has shown consistent improvement since 2022. The southern tributary has contributed most to main stream quality improvements (<i>r</i> = 0.915, <i>p</i> &lt; 0.01). The annual average WQI values across 9 monitoring points ranged from 65.63 to 71.74. The permanganate index (COD_Mn), chemical oxygen demand (COD), and ammonia nitrogen (NH₃-N) were identified as the key pollutants. The 500-m buffer zone spatial scale provided the strongest explanatory power for water quality changes. Artificial surfaces and wetlands were emerged as the most influential land use types. The variations of total phosphorus (TP) concentration exhibits greater complexity compared to other monitored parameters, and its retention mechanisms warrant further investigation in the future. The findings offer scientific insights into water quality management and policy-making for the Huangpu River Basin, which help the policymakers to protect peoples’ health form contaminated water.</p>