Ponds are important habitats for aquatic plants and other biota, particularly in regions where the quality of aquatic ecosystems is deteriorating or even disappearing. Ponds provide refuge for many species and serve as foraging places for others. The ponds studied are located in the Brdo Estate and are under special protection to maintain their educational and other ecosystem services. This study examined the temporal differences (20 years) of the plant communities in eleven ponds concerning eutrophication and/or other human pressures. Various measurements were taken between the two surveys to improve the quality of inflowing water. The selected ponds' physical and chemical parameters, water depth, and transparency were measured. According to our results, water transparency and temperature significantly shaped the structure of the plant community and significantly influenced the presence and abundance of aquatic plants. The changes were reflected in the disappearance of four species of the genus Potamogeton, namely P. filiformis, P. lucens, P. pectinatus, and P. trichoides, which were recorded in 2001 but not in 2021. Secondly, the average number of plant species in the ponds has slightly increased in 20 years, mainly due to emergent plants. The construction of wastewater treatment plants in the catchment area prevented the eutrophication processes.