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Boiling water is the surest way to kill the disease-causing microorganisms in lake or river water, the U.S. Environmental Protection Agency confirms. You can avoid the possibility of nausea, diarrhea or stomach cramps from lake water by filtering it through a coffee filter or several layers of cheesecloth and then boiling it for one minute--or, if at a location one or more miles above sea level, for three minutes. Once the water has cooled, pour it back and forth from one clean container to another to aerate it and improve the taste, if you wish. Store boiled water in clean containers with covers.