Lake ecosystems are important elements of hydrological regime, the quality of these ecosystems is affected by anthropogenic actions, and therefore, a variety of organisms, living in these habitats depend on the applied management solutions. Due to human activities freshwater ecosystems suffer from loss of biodiversity and increased eutrophication. Therefore, important aspects related to lake management include knowledge about the water quality, ecosystem response to climate change as well as increased risks of appearance and spreading of invasive species. Water quality, content of oxygen, nutrients, phytoplankton and distribution of macrophytes, including invasive species were analysed in Balvu and Pērkonu lakes. Presence of invasive species Canadian waterweed (Elodea canadensis) was detected, however, common reed (Phragmites australis) can be considered as expansive species. The analysis of current situation and existing management measures indicates persistent spreading of those species. Significant changes of lake water quality and climate may increase possible spreading of other, more aggressive, invasive species, for example – Nuttall’s waterweed (Elodea nuttallii).