The federal government will pilot a new storm-water runoff policy in three Massachusetts cities. Some big-box stores and malls will need to reduce the rainwater running off their roofs and parking lots. The storm water picks up pollutants and then often contaminates water sources, officials say. "Cities and towns are already investing a lot in storm water," said Ken Moraff, deputy director for ecosystem protection in the Environmental Protection Agency's New England region. "These commercial facilities are missing pieces of the puzzle." One city engineer said, "Large commercial developments that are older will be impacted most significantly."