Wal-Mart Stores Inc. will pay a $3.1 million fine to settle charges of violations of the federal Clean Water Act, the largest civil penalty ever against a company for storm water runoff violations. At 24 store construction sites across the country, the company was charged that it failed to get a permit before beginning construction and did not develop a plan to control polluted runoff water. The retailer was fined $1 million over similar violations in 2001.