River estuaries are connectors of terrestrial and marine ecosystems. Riverine particulate organic carbon (POC) is discharged into oceans after a series of biogeochemical reactions in estuaries. Satellite monitoring of POC will improve our understanding of the carbon dynamics of these water bodies. Based on in situ data from four seasonal survey cruises, we developed an algorithm for estimating POC concentrations in the Pearl River Estuary (PRE). Reflectance ratios, Rrs(678)/Rrs(488) and Rrs(748)/Rrs(412), were set as inputs to calculate POC concentration in the PRE. The algorithm was then applied to MODIS/AQUA data to inverse POC concentrations in the PRE from 2002 to 2014. Additionally, sources, impact factors, and seasonal distributions of POC were also investigated. Phytoplankton contributed more to POC in off-shore waters than that in in-shore waters in autumn and spring, but showed the opposite pattern in winter. Under the influence of freshwater from the Pearl River, underwater topography, tides, winds, etc., the seasonal POC concentrations along a specific section, vertical to water depth gradient, decreased in different seasons. These decreases could be described by exponential functions (y = ae bx , b < 0). The distribution of POC concentrations in the PRE resulted from complex physical and biogeochemical processes, which can change spatially and seasonally.