Farmers, loggers, states — and perhaps most importantly, lawmakers — have rallied in opposition to proposed rules the EPA says are needed to finish the job of cleaning the nation’s waters. Many support a bill to derail the program for at least 18 months.

At the same time, support from environmentalists — who initially embraced the proposal — is waning amid concerns the agency will weaken its final water cleanup rules to soothe opponents.

Nonetheless, the EPA plans to go ahead with the controversial rules, possibly issuing the final version as early as June 30. “The administration is strongly supportive of this rule, and we intend to finalize it in this administration,” J. Charles Fox, EPA assistant administrator for water, said in a recent interview with the Bay Journal.

While critics charge the EPA is moving ahead with a heavy-handed pollution control mandate, Fox said the agency envisions a program in which states bring all sides to the table to custom design plans to clean up specific stretches of water that remain polluted almost three decades after the Clean Water Act was passed.

The sharply different views swirl around cleanup plans known as Total Maximum Daily Loads. A TMDL is a calculation of how much pollution a given are of water can receive and still meet its water quality goal with a margin of error. That pollution level is then allocated among sources so the water standard can be met.

Although TMDLs were supposed to have been done for waterways that failed to meet water quality standards since the original 1972 Clean Water Act, the requirement was largely ignored until environmental groups began winning suits against the EPA in recent years for not ordering them.

But the old rules were vague: Details such as how long states had to write a TMDL — even whether it had to be implemented — were never spelled out.

The EPA sought to clear up those issues in new rules it proposed last August. The proposal gave states up to 15 years to write TMDLs for all their polluted waters. But states would also have to develop implementation schedules for the plans and show “reasonable assurance” that pollution reductions will be made. That could mean enough money to support things like voluntary runoff control programs, or — if needed — new regulations.

Because runoff is the main pollution problem for most impaired waters, critics charged that the EPA, which has to approve all TMDLs, is trying to force states to regulate nonpoint source pollution — something the agency has no authority to do itself. Agricultural and forestry groups, who fear they would be greatly affected, have been particularly hostile. Most of the 34,000 comments received on the proposed rule were in opposition — more than 30,000 came just from the forestry industry.

Fox said the proposal had been the target of a “very aggressive lobbying campaign by the polluters.” He insisted the new rules are needed to “refine and strengthen” the Clean Water Act’s long-overlooked TMDL requirement, which the EPA now views as an important tool to clean up the more than 20,000 water bodies that remain polluted in the United States.

In May, the agency issued a joint statement with the U.S. Department of Agriculture to try to quell some concerns. But in the wake of that statement, environmental support for the rules has softened while criticism from others remains largely unabated.

The statement said the rule will not impose deadlines to attain water quality goals. Environmentalists interpret that as a step back from current rules, which — while not setting a deadline — require continual progress.

The USDA-EPA statement also said states did not have to make proportionate pollution reductions between point sources and nonpoint sources, such as farms, in TMDLs. Environmentalists, wastewater treatment plant operators and business fear that means states would back off on farm runoff controls and instead seek disproportionate reductions from other dischargers.

Those, and other statements, worry environmental groups about what will be in the final rules. “A lot of environmental advocates are asking the question, ‘If it were a take-it-or-leave it situation, would I take it (the new rules) or would I leave it?’” a representative from one organization said. “And a number of groups are saying, leave it.”

Fox, though, said the USDA-EPA statement was not a policy change, but a “clearer articulation of what had been around for some time.”

The EPA never proposed that point and nonpoint sources make proportional pollution reductions. “The only real change is that we never really stated it that explicitly before,” Fox said. “We have always said a state can have the discretion to make its own decisions about how they want to allocate pollution.

“The federal interest is simply making sure it is scientifically defensible, and — under our proposal — that there is a reasonable assurance that you will actually implement that.” At the same time, he said, “everyone needs to be at the table” when a TMDL is developed.

Similarly, Fox said the rule never proposed a specific timeframe for cleanups to be completed — the USDA-EPA statement just makes that an explicit statement. Cleanup timetables depend on local conditions, Fox said. But, he added that while the EPA does not dictate a deadline, all TMDLs must include one. “Each TMDL must identify when that waterbody is expected to meet its standards and it must do so in a timeframe that is as expeditious as possible,” he said.

One thing that the EPA-USDA statement says definitely won’t be in the final rule was a proposed requirement that major new sources of pollution in an impaired waterbody “offset” new discharges by 150 percent. That, in effect, would have forced the establishment of pollution-trading programs in waterbodies.

Industry, environmentalists, and state and local governments found problems with the complexity of the proposal. In its place, Fox said the EPA would offer guidance for an array of ways new pollution sources could be dealt with while a TMDL is developed. The old rule prohibits new discharges until a TMDL is done.

Meanwhile, a bill introduced by Sens. Bob Smith, R-NH, and Mike Crapo, R-ID, would delay the new rules for at least 18 months while the National Academy of Sciences studies the scientific basis behind the calculations used for TMDLs.

Fox said the administration is “flatly opposed” to such a delay. “Obviously, our decisions will get better over time, but I’m afraid if we wait for the better science as many are suggesting that we should do, that is really an excuse for inaction,” he said.

Fox admitted that part of the problem with the TMDL program was that the EPA and the states put them off for so long. By the time lawsuits forced the issue, a staggering backlog of nearly 40,000 TMDLs built up nationwide. Hundreds of the plans are required in each of the Bay states, and the Chesapeake is listed as impaired and, under a court agreement reached last year, will need a TMDL unless it is cleaned up before 2011.

“There is no question in my mind that this problem would be a lot easier to solve if we had been working away at this over the past 20 years,” he said. “It is also true that in the first 20 years of the Clean Water Act, the federal government and the state governments really focused on a lot of the point sources — the big obvious sources of water pollution.”

Now, the focus has switched from those point sources, and many of the waterbodies that need TMDLs are impaired largely by runoff from farms and other land uses. Those sources are often difficult to control, but their combined effect can be as devastating to a waterbody as a discharge pipe. Fox sees the TMDL as the framework in which a watershed plan can be developed to clean up those areas. “What TMDLs really are about is emphasizing that we as a society need to look at the cumulative effects of our activities on the resources around us,” he said.

Fox said he envisions the new rules — with their requirements for cleanup timetables and reasonable assurance that they will be met — as a tool to bring all the local stakeholders in an area together to devise a cleanup strategy.

“What is happening now under the TMDL program — as has happened under the Chesapeake Bay Program for 15 years — is that everyone has a seat at the table in trying to solve a water pollution problem,” he said. “The TMDL is a construct by which everybody sits down and tries to solve a problem, and that is a little different from 20 years ago when it was just a regulatory agency pointing a finger and issuing a permit for a pipe that goes into the river.”

The TMDL process, he said, creates an “accountability structure” that will help waterways finally reach their clean act goals.

If a state fails to write or implement a TMDL, the EPA can take over the job and write new permits for discharges. In areas where most of the pollution is from runoff, the new rules would give it authority to declare large animal feeding operations and specific forestry activities as point sources and require discharge permits. But it still could not regulate diffuse sources of runoff.

In such instances, the agency could provide more grant money to programs that control runoff or — in what Fox called the “absolutely worse case” — withhold certain Clean Water Act funds from the state for not doing the job.

“I firmly believe that if the EPA is doing TMDLs, that’s a bad sign,” Fox said. “I firmly believe that the states should be doing TMDLs in a very collaborative way with local governments. But if for whatever reason that isn’t happening, the EPA does have an obligation to step in and do it.”