Although swimming in Lake Jarun and Lake Bundek has been a long-standing practice of a large number of residents of the City of Zagreb, a certain number of potential swimmers, before the start of the swimming season, have doubts about the microbiological quality of water at swimming areas of these lakes. This thesis compares the results of water quality testing of Jarun and Bundek Lakes with regards to microbiological parameters of E. coli and intestinal enterococci over a five-year period. During this period, a total of 684 samples were analyzed at sixteen locations of Lake Jarun and 126 samples at three locations of Lake Bundek. In swimming areas of both lakes, the lowest percentage of samples of excellent quality with regards to E. coli was recorded in 2014, which was 87 % (Jarun) and 85 % (Bundek). Regarding intestinal enterococci, the smallest number of excellent specimens was recorded at Jarun in 2017 (85 %) and at Bundek in 2015 (83 %). Statistical analysis of the data shows that September is statistically significantly different from other months with regards to both microbiological parameters, and on both lakes. A significant negative correlation was observed between air and water temperatures and E. coli and intestinal enterococci, while 3-day precipitation showed a significant positive correlation with both microbial indicators. Comparing inland water quality assessment across Croatia to the EU, Croatia had 64 % of excellent quality swimming areas compared to 78 % of those at EU level, taking into account the average of all years in the period from 2011 to 2018. The analysis of these results has demonstrated that it is necessary to conduct a systematic monitoring of water quality in order to reduce the risks to human health and to protect the aquatic environment. It is also necessary to educate swimmers and visitors of lakes on how to inform about water quality of the Zagreb lakes, as well as about potentially negative effects in case of poor water quality.