Water turbidity is an important indicator of water quality, which regulates primary production by changing the light field in the water column. Thus, monitoring the spatial and temporal variations in water turbidity is environmentally and biologically important. In this study, nine commonly used spectral index algorithms were tuned using in situ data collected from two field surveys in the Pearl River Estuary of China, and the spectral ratios between the red and green bands (i.e., (Formula presented.) and (Formula presented.)) were selected as the optimal indicator to estimate water turbidity in this region. A long-term environmental data record of water turbidity was established for the Pearl River Estuary by applying the proposed algorithm to MODIS/Aqua data covering the estuary from 2003 to 2019. Water turbidity in the Pearl River Estuary has significantly decreased at a rate of 0.11 nephelometric turbidity units (NTU) per year (R² = 0.84, p < 0.01). The decline in water turbidity is linked with sea-level rise in this area. Sea-level rise may cause the longitudinal and lateral landward retreat of estuarine turbidity maxima (ETMs), directly contributing to the decline in water turbidity. Further, the sea-level rise and the decline in water turbidity in the Pearl River Estuary are also two effects resulting from similar processes, such as urbanization. A high degree of correlation was observed between the water turbidity and salinity, which could facilitate promising monitoring of the increasingly severe saltwater intrusions in this region.