Fourteen years after the federal government acknowledged that Florida had a serious water pollution problem, the U.S. Environmental Protection Agency on Friday agreed to impose new pollution rules to clean up the state's algae-choked waterways — but it may have created a new mess.The Sierra Club, Florida Wildlife Federation and other environmental groups had sued the EPA four years ago over the most persistent water pollution problem in Florida — one that the federal agency had first told the state to do something about in 1998.When the EPA settled the suit, it agreed to impose tough new pollution rules, prompting a political backlash from Gov. Rick Scott, big business, agricultural interests, paper mills and utilities, among other interests.Environmental groups had pushed for the EPA to stick to its guns. Meanwhile, state Department of Environmental Protection officials negotiated with the EPA to instead adopt the rules that those industries had agreed to follow.Late Friday night, the EPA said in a news release that it had approved the state rules for part of the state's waterways, but would still impose the federal rules for the rest. According to David Guest of Earthjustice, that means the state rules cover only 15 percent while the new federal rules cover 85 percent — about 100,000 miles of waterways.State DEP officials said they were disappointed the EPA would impose federal rules on any part of the state and vowed to "work with them to craft solutions" to put the state in charge of all pollution rules.The move signals the end of a lengthy court and political battle over the new pollution standards, and the environmental activists involved hailed the decision."We fought every polluting industry in Florida for four years to get to this result," said Guest, who represented environmental groups in pursuing a lawsuit based on a 1998 EPA finding. The EPA decision, which sets a nationwide precedent, also marks a first step toward changing many aspects of current Florida life, including how suburban lawns are fertilized and the way stormwater runoff and sewage are treated by local governments.The next step will be for EPA officials to draw up guidelines for Florida's counties and cities on how they should implement the new rules, said Frank Jackalone of the Sierra Club, one of the plaintiffs in the suit. One example he cited that counties and cities may choose to follow: Pinellas County's ban on the sale of fertilizer during the rainy summer season.The EPA's decision concerns trying to control what has become, over the past three decades, the most common water pollution problem in the state: nitrate or nutrient pollution. Every rainfall washes nutrients such as phosphorous and nitrogen into Florida's springs, lakes, rivers and estuaries from over-fertilized lawns and golf courses, leaking septic tanks, malfunctioning sewer plants, dairy farms and cattle ranches.The pollution has fed the increase in toxic algae blooms that sometimes kill thousands of fish and cause rashes and respiratory problems among swimmers, boaters and beachgoers. As the Tampa Bay Times explained in an investigative report on Sunday, pollution-fueled algae blooms now choke many of the state's most popular springs. Yet Florida's long-standing rules on controlling nutrient pollution were vaguely worded guidelines and not the numeric criteria needed to strictly limit it, Earthjustice said in its 2008 lawsuit. The EPA had told Florida and all the other states in 1998 to set numeric nutrient standards, but when they failed to comply the federal agency failed to follow up, Earthjustice noted in the suit.The EPA settled in 2009 and a year later unveiled 168 pages of region-specific pollution standards, saying they could cost Florida residents an extra 11 to 20 cents a day per household. Opponents charged it would be more expensive than that. Scott, along with U.S. representatives and senators and state legislators, contended that the pollution limits would ruin the state's economy. One business leader asked, "How clean does our water have to be?"EPA officials responded by repeatedly delaying when those standards would take effect and negotiating with state officials on alternative standards for some 100,000 miles of Florida waterways.U.S. District Judge Robert Hinkle told them this summer that they must act by a Friday deadline, prompting the EPA to file the notice that it would seek no further delays.