The canyon and the Rječina valley is a very important ecosystem, which is partly included in the Natura 2020 ecological network and thus obligates to preserving the existing biodiversity. Economic development has led to the transformation of the Rječina river, and numerous illegal landfills as well as wastewater from municipal, industrial and agricultural areas further impend the services of this ecosystem and have an impact on biodiversity. The goal of the research: The aim of this study was to evaluate the water quality of the middle and downstream course of the Rječina river using the Allium cepa test. Materials and methods: Water sampling was carried out at two stations in the middle and downstream course of Rječina during September 2017. Cytotoxicity was assessed based on onion root growth (incidence of inhibition and mitotic index), while genotoxicity was evaluated based on the number of chromosomal aberrations. Results: Decreased growth of meristem cells of the onion root and a lower mitotic index in the middle and downstream courses of the Rječina compared to the negative control were found. The number of chromosomal aberrations is highest in the downstream. Conclusion: The measured biological effect of water Rječina on the meristem cells of the onions indicate the presence of cytotoxic and genotoxic substance, which need to be verified by other methods. Systematic biomonitoring of the water ecosystem in order to sustain the ecosystem services and its biodiversity should be included to improve water quality management.