During the last decades, anthropogenic pressure on freshwater ecosystems has significantly increased. To a large degree, such impacts are related to contamination by toxic elements and nutrients. In the long term, pollution results in a decrease in biodiversity and leads to the loss of balance in complex environments, disrupts or even destroys natural self-regulatory mechanisms, and often causes irreversible changes at different levels of biological organization. Small urban lakes are subject to exceptionally high, long-term anthropogenic impacts. At the same time, these water bodies are intensively used for social purposes and provide a wide range of essential ecosystem services. There is a considerable lack of research on small urban lakes, as most national monitoring surveys are carried out on lakes larger than 50 ha, according to the Water Framework Directive (2000/60/EC) recommendations. The thesis will aim to assess the ecological status of small urban lakes; by determining the concentrations of hazardous pollutants in sediments and biota, bloom-causing algae and their toxins, and by investigating geno-, cytotoxicity, and biochemical parameters in bioindicator organisms. Background levels of studied parameters will be determined in lakes, which are located at some distance from sources of contamination and, based on the results of the chemical analysis, are considered as not polluted. The impact of toxins released during water blooms will be assessed under laboratory conditions. Active monitoring experiments will be performed in situ by translocating bioindicator organisms to the lakes affected by long-term severe contamination, aiming to assess the level of adaptation of local, aboriginal organisms and to determine the true values of studied biomarkers. The research in this thesis should initiate significant changes in the monitoring, protection, and management of small urban lakes.