Surabaya River is one of the lower tributary of the Brantas, which is included as the top 20 plastic polluted rivers worldwide. The main function of Surabaya River is for raw water source for Surabaya City. Besides, this river is used for domestic and industrial waste discharges, and for irrigation. This study aimed to investigate the distribution of microplastics (MPs/MP) and its characteristics in three stratified depths (surface, middle, and bottom) of the river. This study was conducted in eight sampling sites, which were located in the Lower Brantas and the Surabaya Rivers. The MP abundance in the surface, middle, and bottom of the river ranged 1.47–43.11; 0.76–12.56; and 1.43–34.63 particles/m3, respectively. The highest average of MP abundance was 21.16 particles/m3 at the lower end of the river. The MP particles tend to be mainly distributed in the surface than in the other depth levels. The MP particles in each depth were generally dominated by film shaped large MP of 1–5 mm size, and transparent in color. Three main polymer types of the MPs were low density polyethylene, polypropylene, and polyethylene.