The effluents from the water treatment station of REGIDESO located in Kingabwa (Kinshasa city) are accused of reducing aquatic biodiversity of Matete and N'djili rivers and are responsible of some human diseases. The effects of these effluents on the physico-chemical and biological quality of water of Matete and N’djili rivers were evaluated. The benthic macro-invertebrates and Gambusia affinis were used as biodiversity richness indicator and model system for toxicity assays. The analyses of physicochemical parameters revealed a constant temperature in the stations studied (± 25 °C) and a high value of conductivity in the sites near the effluents discharge location. On the whole of the sites, the bacterial load was reduced to the neighboring sites of the effluents discharge. The pH is slightly acidic depending on the period and the sampling sites. Dissolved oxygen decreases as sampling seasons. 1405 specimens of benthic macro-invertebrates including 499 in the rainy season and 906 in dry season were harvested. The Shannon index value ranges from 0.4 to 2.9 during rainy season and 1.7 to 2.9 during dry season, reflecting the passage of polluted water to moderately pollute in rain season and moderately polluted to slightly pollute in the dry season. The toxicity bioassay revealed that these effluents are toxic (LC50= 0.109%). It is thus desirable to install a monitoring system near of the station of water purification of the REGIDESO N’djili in order to regularly control the dangerosity of the effluents poured in the surrounding watery ecosystems.