The pollution of freshwater environments with microplastics (MPs) has attracted increasing attention owing to their threats to aquatic ecosystems and human health. Here, we sampled and analyzed MPs from mainstream, tributary, and backwater areas in the Wanzhou section of the Three Gorges Reservoir (TGR) in impoundment and flood periods. Microplastic pollution was the most severe in the backwater areas. The average abundance of MPs reached the highest value in the flood period (5.27±3.47×107items km−2), which was 3–5 times that in the impoundment period. In the 0.3–5 mm size class, the 1–5 mm fraction was the most abundant, accounting for more than 81% in the flood period and 68% of the total MP particle abundance in the impoundment period in the mainstream and backwater areas. However, 0.3–1 mm MPs contributed more than 50% in the tributaries during the impoundment period. Polystyrene, polypropylene, and polyethylene MPs were detected in foam, fragment, sheet, and line-shaped MP particles. White, opaque, foamed polystyrene MPs contributed 32–81% to total MP particle abundance in the watershed. Microplastic particle surfaces showed signs of damage and oxidation, and ten different elements were found. Oxygen was clustered on the surface of foam and fragment MPs. Microplastic pollution was severe in the Wanzhou watershed. Especially in the backwater areas, oxidized MPs of variable shapes derived mainly from surface runoff in the flood period and sewage discharge in the impoundment period were abundant. The results of this study contribute to understanding seasonal pollution patterns and surface characteristics of MPs in the TGR and similar watersheds.