From the rulebook: "In the game, each player assumes the role of a water pollution control official who is responsible for stocking his lake. He does so by collecting appropriate organisms as he moves around the game board, confronting the problems of water pollution each time he lands on a 'pollution' triangle. Throughout the game he must learn to anticipate possible pollution of his lake, attempt to avoid the problem of overpopulation, manage his finances efficiently, and consider the problem of possible pollution coming from upstream. A player wins the game by controlling water pollution successfully and thereby being the first to completely stock his lake."
Each player is the Commissioner of Water Pollution for their own lake. Each lake is connected by a series of rivers and surrounded by potential polluters. The first player to completely stock his lake with organisms while controlling the pollution from the nearby community of farms, industries and residential developments is the winner. Clean Water acquaints players with some of the complexities involved with dealing different types of pollutants while maintaining a healthy ecosystem.
Players roll a die to move around the board and collect organisms for their lakes. Landing on a pollution space will kill off some of the higher organisms and increase the lower organisms, but players can purchase Abatement cards to try to avoid the pollution. Overpopulation of any one type of critter will also disturb the ecology, but players can occasionally exchange lower organisms for higher ones. Players also have opportunities to bid for federal funding. The first player to fill his lake with the required organisms wins the game.