Introduction: According to the national classification of Croatia, karst ponds are small and temporary accumulations of water that can dry up and are usually formed by the accumulation of rain on impermeable or semi-permeable soil. They can occur naturally or through anthropogenic intervention and have been designated by Nature 2000 as the most important habitat for the conservation and maintenance of biodiversity. The aim of this study is to assess the water quality of two karst ponds in the Krasica region using the Allium cepa test. Materials and methods: Two ponds in the localities of Veternjak and Hroljevo were selected for water sampling and sampling was carried out on 29 April 2023. The cytotoxicity of the water in the ponds was determined by the growth of meristem cells of onion roots, i.e. the frequency of growth inhibition. Physicochemical parameters (temperature and pH) and air quality were also determined Results: A statistically significant difference was found in the growth of onion roots in the water samples from the Hroljevo pond compared to the negative control, indicating the possibility of the presence of cytotoxic substances in the water. Based on the degree of inhibition of onion root growth, it was found that the water from the Hroljevo pond belongs to the group of β-mesotoxic waters, indicating moderately toxic water, while the water from the Veternjak pond belongs to the oligosaprobic waters, indicating slightly polluted water. Based on the measured pH values, it was determined that both ponds belong to the eutrophic type of habitat. On the day of sampling, as well as during the entire week prior to sampling, elevated levels of hydrogen sulphide (very poor) and ozone (moderate) were measured at the air quality monitoring station in Krasica. Conclusion: Biomonitoring to improve ecosystem services and own sustainability as well as to maintain biodiversity should be part of the continuous monitoring of the quality of small aquatic ecosystems.