That depends on the type of pollution. Some pollution can be digested by microorganisms. Since microorganisms occur naturally in our waters, In that case the solution is just to wait for them to digest the pollutants. However, if the waters are overburdened with waste, the microorganisms may consume all the dissolved oxygen in the water, causing the aquatic ecosystem to collapse.
As for non-organic pollutants, those must be treated on a case-by-case basis. People can induce chemical reactions to render them less harmful or precipitate and filter them out of the water.
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