The studies on acidification of the lakes in the Tatra Mountains started parallel by teams of the Institute of Fishery Research and Hydrobiology, Bratislava and of the Department of Hydrobiology, Charles University, Prague (The Czech Republic) in the beginning of the 80-s. In the year 1991 started the international project AL:PE (Acidification of Mountain Lakes: Palaeolimnology and Ecology), funded by the European Commission Environment Programme. In the years 1994-1996, in its second part, AL:PE2 (Remote Mountain Lakes as Indicators of Air Pollution and Climate Change), also the Slovak lakes in the High Tatras - Starolesnianske pleso and Nizne Terianske pleso were involved. It was the first comprehensive study of remote mountain lakes at the European scale in which institutes from 11 Europe countries were involved and 19 lakes were studied. The AL:PE project assessed the status of remote mountain lakes throughout Europe on the basis of sediment core records and chemical and biological surveys. The next project MOLAR (Mountain Lake Research - Measuring and modelling the dynamic response of remote mountain take ecosystems to environmental change) as continuation of previous projects allowed detailed limnological studies on chosen lakes. The main aim of this project was to develop predictive models for acidity, pollutant flux and climate variability. Research of Nizne Terianske pleso was a part of project focussed on climate variability and ecosystem dynamics at remote alpine and arctic lakes. In the present time the new project EMERGE (European Mountain Lake Ecosystems: Regionalisation, Diagnostics & Socio-economic Evaluation) has started specific objectives of which are to assess the status of remote mountain lake ecosystems throughout Europe following the requirements of the EU Water Framework directive and providing an evaluation of the findings in ecological, environmental and socio-economic terms. Remote mountain lakes are excellent sensors of environmental changes, and their high quality sediment records can be used to infer the speed, direction and biological impact of changing air quality and climate. For those reasons it is very important to make long-term research of remote mountain lakes in the framework of co-operation of the European countries and to continue in the next scientific studies also in future.