The concentration of chlorophyll-a (CHL) is an important proxy for the amount of phytoplankton biomass in the ocean. Characterizing the variability of CHL in the Pearl River Plume (PRP) is therefore of great importance for the understanding of the changes in oceanic productivity in the coastal region. By applying quantile regression analysis on 21-year (1998–2018) near-surface CHL data from satellite observations, this study investigated the long-term trend of CHL in the PRP. The results show decreasing trends (at an order of 10−2 mg m−3 year−1) for all percentiles of the CHL in the PRP, suggesting a decrease in productivity in the past two decades. The trends differ fundamentally from those in the open regions of the northern South China Sea with mixed signs and small magnitudes (10−4 mg m−3 year−1). The magnitudes of the trends in high quantiles (>80th) are larger than those in low quantiles (<50th) in the PRP, indicative of a decrease in the variance of the CHL. The area with apparent decreasing trends is restricted to the PRP in summer and extends to the entire coastal region in winter. This decrease in CHL is possibly attributed to the decrease in nutrient input from the river runoff and the weakening of wind-forced mixing rather than the changes in sea surface temperature. This study extends our knowledge on the variability of CHL in the PRP and provides references to the investigation of the changes of the coastal ecological environment.