Microplastic (MP) contamination has appeared as pollution of global concern in the aquatic as well as the terrestrial environment. In India, very few studies are available on MP load in freshwater ecosystems despite knowing the fact that rivers play a major role in transporting MPs into the marine ecosystem. This research estimates a load of MP in water and sediments of disappearing tributaries (Suswa, Rispana and Bindal) of the River Ganga at Dehradun, India. The water and sediment samples were collected from 22 locations and analyzed for MP occurrence and characterizations (size, shape, polymer types, and colour abundances) and physicochemical parameters as well. The average MP load was found to be in the ranges of 7200–16,400 items/kg in sediments and 2800–4200 items/L in water in the studied sites. The highest MP load occurred in Suswa followed by, Rispana and Bindal. ATR-FTIR analysis revealed polyethylene (PE) and polypropylene (PP) as the dominant polymer groups of MP in the studied sites. Fibers/ threads (41%) were the dominant shapes found in water samples while fragments (38%) were in the case of sediment. White and black colour MP occurred in the highest amount in both water and sediments. Principle component analysis suggested the mixing of urban runoff and sewage as the major contributors of MPs in studied tributaries. In summary, illegal dumping of urban solid waste in river catchment areas, human encroachment near the river sides, direct disposal of sewage and industrial effluents, etc. could be a major source of MPs in such urban rivers.