The Pearl River estuary is an ecologically dynamic region located in southern China that experiences strong gradients in its biogeochemical properties. This study examined the seasonality of nutrient dynamics, identified related environmental responses, and evaluated how river discharge regulated nutrient sink and source. The field investigation showed significant differences of dissolved nutrients with seasons and three zones of the estuary regarding the estuarine characteristics. Spatially, nutrients exhibited a clear decreasing trend along the salinity gradient; temporally, their levels were obviously higher in summer than other seasons. The aquatic environment was overall eutrophic, as a result of increased fluxes of nitrogen and silicate. This estuary was thus highly sensitive to nutrient enrichment and related pollution of eutrophication. River discharge, oceanic current, and atmospheric deposition distinctly influenced the nutrient status. These factors accordingly may influence phytoplankton that are of importance in coastal ecosystems. Phytoplankton (in terms of chlorophyll) was potentially phosphate limited, which then more frequently resulted in nutrient pollution and blooms. Additionally, the nutrient sources were implied according to the cause–effect chains between nutrients, hydrology, and chlorophyll, identified by the PCA-generated quantification. Nitrogen was constrained by marine-riverine waters and their mutual increase-decline trend, and a new source was supplemented along the transport from river to sea, while a different source of terrestrial emission from coastal cities contributed to phosphate greatly.