Abstract: Deterioration of water quality and quantity is a world-wide problem. To prevent global water crisis, the European Water Framework Directive (WFD) requires that all European countries monitor aquatic ecosystems and ensure their good ecological status by 2015. Traditional methods of assessing water quality were mainly based on physico-chemical parameters of water, while WFD stresses importance of biological indicators and requires ecosystem approach within the whole water basin. With modern hydroacoustic equipment one can get not only detailed information on fish abundance, individual sizes, behavior, spatial and temporal distribution patterns, but also information on height, abundance and distribution of underwater vegetation and characteristics of bottom substrate. The acoustic measurements of fish and macrophytes were performed in 4 lakes of the river WEL catchment using Simrad split beam echosounder EK60, 70 kHz. Several acoustic metrics such as fish abundance, bubbles abundance and max vegetation depth were used as acoustic indicators of lake quality and compared with classification systems based on other quality indicators. The results have shown that hydroacoustics is a promising tool for monitoring and mapping an ecosystem.