Studies focused only on surface water may underestimate microplastic abundance in aquatic environments. This was the first survey to investigate the vertical (surface, intermediate, and bottom waters) distribution and composition of microplastics (MPs) in the water columns and surface sediments collected from an urban seagoing river in northern China. Microplastic abundance in the water columns ranged from 5.6 to 31.4 items∙L-1 and from 2141 to 10035 items∙kg-1 dry weight (dw) in the surface sediments. Polyethylene dominated throughout the water columns to the surface sediments, in which low- and high-density polyethylene (LDPE and HDPE) were dominant in the water columns and surface sediments, respectively. The dominant shape of MPs was fibers/lines in both the water column and the surface sediment samples. Different from the estimations, the average abundance of MPs in the surface and intermediate waters was significantly lower (p < 0.01) than that in the bottom water, which may be due to the resuspension of small-sized MPs in the bottom water. As the MPs size increased, their vertical distributions in the water columns were more affected by the water depth. The results showed that MPs were detained in the water columns of river system, and the high concentrations of MPs in the bottom water could not be neglected.