Distribution of Transparent Exopolymer Particles (TEP) in the Pearl River estuary, China, was investigated during two cruises in August 2009 and January 2010. TEPcolor concentrations were 521.5–1727.4 μg Xeq.L−1 (μg Gum Xanthan equivalent liter−1) in August 2009 and 88.7–1586.9 μg Xeq.L−1 in January 2010, respectively. The size of TEP generally increased in the seaward along the longitudinal section with the dominant size of 2–40 μm during the cruises. Experimental work suggested that both concentration and size of TEP increased with Ca2+ concentration (from 0.8 mmol L−1 to 10 mmol L−1). In the field study, Ca2+ concentration had a positive correlation with TEPcolor concentration in the surface layer with salinity <16. Decrease of TEP concentration seaward from intermediary salinity was partly due to dilution of seawater as well as enhanced aggregation and sedimentation of TEP via increasing divalent cation concentration. TEP concentration and turbidity maximum coexisted at the tip of salt wedge in the bottom layer during the wet season, and positive correlation between TEP and turbidity was observed in the winter. Relationships between TEP and turbidity suggested the important contribution of TEP aggregation to flocculation and sedimentation of particles in estuaries. Different pattern of TEP during two cruises can be attributed to physical process (i.e., mixing type) in estuaries. These findings indicated that formation and distribution of TEP were largely influenced by interaction between physical and biogeochemical processes in the Pearl River estuary. A conceptual model for TEP formation and distribution in the Pearl River estuary was developed.