Water resource contamination is still a major concern in several regions of developing countries, especially in the Democratic Republic of Congo (DRC) in which polluted waters poses serious risks to human health and the environment. The aim of this study was to assess the inter-annual and seasonal changes in physicochemical, bacteriological parameters and community composition of macroinvertebrates in the rivers in Mikeno sector. The physicochemical parameters analysed, including pH, temperature, electrical conductivity, total dissolved solid, total suspend sediment, dissolved oxygen, biological oxygen demand after 5 day incubation, chemical oxygen demand, alkalinity, total hardness, calcium hardness, magnesium hardness, chloride, sulphate, total phosphorus, soluble reactive phosphorus, total nitrogen, ammonia, nitrate and trace of heavy metals collected from rivers and springs in Mikeno sector using standards methods for water analysis during the period of two years (2015-2016). The results indicate the annual and seasonal difference in the physicochemical composition of water. All physicochemical values in general, analysed in the springs and rivers were low during the sampling period in the two years. Water analysed during the two seasons appear to meet drinking water standards, according to the WHO guidelines. But for bacteriological aspect some springs contained a high coliform count and need to have specific treatment before to be used for drinking. Rwinkwi River had a high species richness with 19 taxa and Nyabisika River was poor in macroinvertebrate. This study is important for the present situation and can be applied in similar environmental compartments in the future to assess the availability of safe drinking water in developing countries.