In March and April 1993, thousands of Milwaukee, Wisconsin, residents became ill after the city’s water supply was infected by an outbreak of Cryptosporidium, a parasite commonly found in the feces of dairy calves. Runoff from the spring thaw and heavy rains was thought to have carried contaminants from the Milwaukee area’s many dairy farms into Lake Michigan, the city’s water source. The outbreak caused the deaths of fifty people with weakened immune systems and sent thousands to area hospitals. The event drew attention to the problem of “nonpoint” sources of water pollution—that is, polluted runoff from farms, construction sites, city streets, sewer systems, and other sources— affecting up to half of the nation’s waters.

In the thirty years since the passage of the Clean Air Act of...