Spatio-Temporal Variability of Key Habitat Drivers in China’s Coastal Waters

China’s coastal fisheries face challenges to their sustainability due to climate and human-induced pressures on key habitat drivers. This study provides an 18-year (2003–2020) assessment of six key ecological and data-available environmental factors (sea-surface temperature (SST), salinity, transparency, currents (eastward velocity, EV; northward velocity, NV), and net primary productivity (NPP), selected for their ecological relevance and data availability, across the Bohai, Yellow, and East China Seas at a spatial resolution of 0.083°. Non-parametric trend tests and seasonal climatologies were applied using MODIS-Aqua and CMEMS data with a refined quasi-analytical algorithm (QAA-v6). The results show distinct gradients: SST ranging from 9 to 13 °C (Bohai Sea) to >20 °C (East China Sea); transparency ranging from <5 m (turbid coasts) to 29.20 m (offshore). Seasonal peaks occurred for SST (summer: 18.92 °C), transparency (summer: 12.54 m), and primary productivity (spring: 1289 mg/m2). Long-term trends reveal regional SST warming in the northern Yellow Sea (9.78% of the area), but cooling in the central East China Sea. Widespread increases in transparency were observed (65.14% of the area), though productivity declined significantly (27.3%). The drivers showed spatial coupling (e.g., SST–salinity r = 0.95), but the long-term trends were decoupled. This study provides a comprehensive and long-term assessment of multiple key habitat drivers across China’s coastal seas. The results provide an unprecedented empirical baseline and dynamic management tools for China’s changing coastal ecosystems.