Abstract: To address the concern that the habitat-use patterns of Indo-Pacific humpback dolphins (Sousa chinensis) in the Pearl River Estuary may produce adjustments under long-term multiple stressors, we calculated survey effort-corrected dolphin density (DPSE) based on line-transect survey data collected during three periods: 2015–2016, 2018–2019, and 2024–2025 Grids with DPSE values greater than 60 were defined as high-use habitats to compare their proportional distribution inside and outside the reserve, while group and individual encounter rates were simultaneously quantified. A total of 30 surveys were completed, covering 10,330.22 km of transects. Group encounter rates varied little among stages 5.10–5.85 groups·(100 km)⁻¹, whereas individual encounter rates were 30.65, 24.22, and 27.09 individuals·(100 km)⁻¹ in 2015–2016, 2018–2019, and 2024–2025, respectively, showing a decrease followed by a slight increase. The proportion of high-use habitat grids located within the reserve decreased from 34.7% in 2015–2016 to 18.4% in 2024–2025, indicating reduced spatial overlap between high-use grids and the existing reserve boundary in the stage-aggregated results. Overall, the stage-level spatial use pattern of dolphins changed through time, and the reserve's coverage of high-use habitats changed accordingly. It is recommended that interannually repeated high-use grids be prioritized as key supervision and management units, and long-term high-use areas outside the reserve be continuously monitored, so as to improve the actual protective coverage of critical dolphin habitats.