Microplastic (MP) pollution in aquatic ecosystems poses significant ecological and public health risks. A comprehensive understanding of estuarine MP pollution, influenced by multiple anthropogenic and environmental factors, remains elusive in current research. This study investigated the spatial distribution patterns and dominant factors influencing MP abundance (MPA) and physicochemical diversity in the river water and sediments of the Pearl River Estuary (PRE), while also assessing the associated ecological risks. The dominant MP categories in river water and sediments were fibers, clear in color, <1 mm in length, and composed of polyethylene terephthalate and polypropylene. Whereas inland regions showed higher MPA, nearshore regions exhibited marginally greater physicochemical diversity. Multivariate statistical analysis identified population density as the primary driver of both MPA in river water and MP physicochemical diversity in sediments. MP physicochemical diversity in river water was predominantly governed by the synergistic effect of salinity and the vegetation land. MPA in sediments depended on the synergistic effect of flow rate and watershed area. Ecological risk assessment identified elevated risks in the eastern study area driven by the presence of polymethyl methacrylate. This study establishes a scientific basis for PRE region MP management and provides global comparative data for estuarine MP research.