The publication is addressing the problems of pollution from agricultural sources; municipal wastewater and industry in line with the bacterial pollution caused by migratory waterfowl of Paliastomi Lake that is an internationally recognized habitat, wintery and transit area of the birds and an important tourism site. It reviews: the current state of the environment of Paliastomi Lake at the moment of the chemical and microbiological research and mathematical simulation modeling of possible dissemination of polluting chemicals and bacterial pathogens; pollution by nutrient-rich water causing large blooms of algae and aquatic plants that in its turn leaves little oxygen for fish and other aquatic animals, resulting in the eutrophication followed by suffocation of aquatic life.