A study was carried out to assess the pollution load in river Yamuna at Mathura (U.P.) and its impact on population size of some aquatic microbes. The key indicators of sewage waste load were Coliform count (MPN), BOD, sulphates, chloride and ammonia. The susceptible microbes that were analysed included Ulothrix, Paramecium spp. Difflugia sp. and species of Cyclops. The study revealed that the river is very badly polluted especially with sewage, garbage and effluents from city and local industries. The population of Coliform bacteria and Ulothrix (algal organisms) was found very high in those areas, where organic pollutants were very high in amount. But other organisms like, Paramecium spp. Difflugia spp. and Cyclops exhibited a severe decline in population count, indicating heavy pollution load, especially during summer months.