The environmental disturbances due to human activities increase in many countries and draw away various types of water pollutions. These pollutions are important and cause a serious regional and local problem in public health. In Bukavu and the surrounding areas, there are enough aquatic systems which shown signs of pollution resulting from human activities. In order to estimate the impact of human activities on the water quality within rivers, this study was carried out in the Kahuwa river, located in Bukavu, urban area, and Mpungwe river, located in rural area, so far at 20 Km of Bukavu. The physico-chemical and biological parameters from 7 sampling sites of both rivers (4 in the Kahuwa river and 3 in the Mpungwe river) was assessed in-situ and in the laboratory of the Lwiro Research Centre in Natural Sciences, Democratic Republic of Congo. According to the results obtained, Kahuwa river is more polluted than Mpungwe river during the period of this study. The physico-chemical parameters reach from upstream to downstream in both rivers Kahuwa and Mpungwe. The nutrients (phosphorus and nitrogen) increased in the sites which is intensively anthropogenic activities (Kibonge, Cheche and SNCC for the Kahuwa river and Murhesa factory for the Mpungwe river). The organic pollution is intensified by anthropogenic used. In general the physico-chemical water quality parameters show a significant difference (p <0,05). The major sources of the high levels of nutrients are in general the waste dumping, the mechanical erosion of rocks and soil particles due to agriculture blocks, the septic hole, the domestic sewers and industrial effluents in the water bodies, which are not regulated. The taxanomic diversity presents fewer species in Kahuwa river (14) than Mpungwe river (31). The difference is significant between both rivers (p <0,001) as regards species richness. The water quality was found to be the major factor contributing to the species richness of Kahuwa river and the impact of agriculture land use in the catchment on benthic macroinvertebrates distribution is significant. The several diversity (Shannon-Weaver, Hilsenhof, Simpson and Maragelf Indices) and pollution biotic macroinvertebrates indices show variations of the population diversity between the samples sites and rivers. In order to reduce the organic materials loading from Kahuwa micro catchment and Lake Kivu, there is need of erosion prevention and sanitation program (VIP toilet).