The estuary is regarded as a bond between the river and the ocean, microplastics are recognized as worldwide contaminants and abundant in the surface water and sediments in estuarial and coastal areas. Most quantification of microplastic fluxes from the river to the sea were evaluated by the water-pathway riverine input. However, the atmospheric deposition and the underground water input were ignored. Some literature reported the atmospheric deposition of microplastics in the estuary could contribute to 7% in the coastal area. Here, we study the pollution characteristics of microplastics in riverine water, underground water, dry and precipitation samples collected from Jiulong river estuary near Xiamen, a subtropical coastal city in Fujian province, China and evaluate the fluxes from the river to the sea. This paper is the first report on the quantification of microplastic fluxes to the sea based on the different pathway, also the seasonal variation of microplastics were also discussed.