In West Africa, particularly in Burkina Faso, the urban freshwater bodies are amongst the most threatened exacerbating the urban environmental crises. Domestic and industrial discharges and fecal sludge are the main sources of urban water pollution. This systematic pollution, which deteriorates the physicochemical and biological condition of urban water ecosystems is a major concern for decision-makers and scientists. Thus, this study was undertaken to assess the effects of urban wastes on ecological status of physicochemical parameters et biological organisms. To do so, from September to October 2020, physicochemical and bacteriological parameters were analyzed using standard methods. Then, the macroinvertebrates were collected using hand net, and then identified in the laboratory. The results showed that the concentrations of physicochemical variables such as conductivity, COD, BOD5, nutrients and chlorides were high in downstream compared to those in upstream. The higher concentrations of total coliforms, Escherichia coli and faecal streptococci were reported in downstream. In regard of macroinvertebrates, the results revealed that taxonomic richness, the relative composition of polluo-sensitive taxa and the Shannon-Wiener index were very low in downstream. From our results, the urban freshwaters ecosystems are strongly impacted including waterborne diseases spreading, and for suitable management of these waterbodies and the well-being of riparian’s population, it is crucial to strengthen the legislation on the discharge of domestic and industrial waste, and to promote appropriate systems for the waste treatment in our cities, and to train and raise public awareness of environmental citizenship where ecology meet society.