When Lisa Jackson takes the helm of the federal Environmental Protection Agency next month, she will face some of the most pressing issues of our time: climate change, air pollution, Superfund.

And that's just for starters.

The agency itself is battered and bruised by a string of regulatory missteps, a tangle of legal challenges, and deep cuts to a staff of dispirited scientists.

"She has a big job," said Carl Pope, executive director of the Sierra Club. "She's inheriting an agency that is badly demoralized, heavily criticized, and one with a greatly weakened capacity."

He said virtually every air-pollution rule the EPA had put forward over the last eight years had been thrown out by the courts, as was detailed in an Inquirer series, "Smoke and Mirrors," which ran this week.

"The to-do list for the Obama administration is truly massive," said Frank O'Donnell, president of Clean Air Watch in Washington. "They have to basically mop up a lot of problems before they get to their initiatives. And they are high priority."

Although Jackson has not been formally named, her nomination has been widely reported, based on anonymous sources close to the Obama camp.

Global warming will likely be at the top of her list.

Eileen Claussen, president of the Pew Center on Global Climate Change, predicted Jackson would soon grant a waiver to California to further limit auto emissions.

That would let New Jersey, Pennsylvania and other states do the same, ultimately forcing a national law.

O'Donnell and Claussen also said the agency would have to push for a ruling on whether carbon dioxide and other greenhouse gases imperil the public welfare by contributing to global warming.

Under the current administrator, Stephen L. Johnson, the EPA made a draft finding supporting that, but the Bush administration refused to accept it, forcing Johnson to produce a much weaker one.

A stronger finding would trigger the nation's first global-warming regulations, likely including emission standards on automobiles and power plants.

"It's one tangible way to make progress on global warming right off the bat without legislation," O'Donnell said.

Jackson likely will also have to devise a federal cap-and-trade program for industrial emissions. Her experience on the executive board of the 10-state Regional Greenhouse Gas Initiative should help.

"Lisa was instrumental in making sure the caps were set in a certain way that allowed industry time to adjust, but held firm to the fact that there were going to be caps, and those caps would be declining, and business as usual was no longer acceptable," said Ralph Izzo, president of Public Service Enterprise Group Inc. (PSEG), a New Jersey energy company. He called it "a reasonable approach."

One test will be how well she works with the other top environmental and energy officials, including physicist Steven Chu as energy secretary; Nancy Sutley, a Los Angeles deputy mayor, as head of the White House Council on Environmental Quality; and Carol Browner, a former EPA administrator, as energy "czar."

"They're setting up a situation where there will be many cooks in the climate-change kitchen," said Frank Maisano, an energy specialist who works with refineries, utilities and wind developers.

Brian F. Keane, president of SmartPower, a national nonprofit that promotes renewable energy, says he thinks Jackson and the others can handle it. "I think she's shown in New Jersey that she can do that. These are collaborative, cooperative people."

Before Johnson's appointment in 2005, virtually every administrator came from outside the agency and had extensive political experience.

The Bush administration said Johnson was different. He was heralded as a scientist and agency insider who had risen through the ranks.

But Johnson acquiesced to the president on key policy issues, such as global warming, leaving his staff frustrated and demoralized.

Jackson represents a new step in the evolution of the EPA administrator's position.

She has both scientific training - a master's degree in chemical engineering from Princeton - and strong political experience. She worked at the EPA for 16 years, led a state agency, and as of Dec. 1 had become Gov. Corzine's chief of staff.

She also has experience with heightened expectations and dwindling reserves.

The EPA budget dropped from $9.5 billion in 2001 to $7.1 billion in 2009.

During Jackson's nearly three years at the DEP, the department bled nearly 400 jobs, reducing it to staffing levels not seen in a decade.

The latest DEP budget of $435.7 million came after cuts of $46.7 million - or 9.7 percent. In April testimony to the state Legislature, Jackson lamented that "the current budgetary situation combined with decades of statutory mandates – many funded, but many not – is forcing us into a 'do less with less' approach."

Jackson considered closing nine parks to save $4.5 million but eventually backed off. She instead used surplus beach-replenishment money, angering Shore towns.

Corzine yesterday praised her ability to make do. "She's an appropriate defender of carrying out the mission," he said, but she also understands that "we don't have the ability to spend dollars we don't have."

Another key rule that the new administrator will confront is the Clean Air Interstate Rule - or CAIR - which is mired in court.

Before CAIR, states were asked to meet certain air standards. But it was virtually impossible for states such as New Jersey, which is at the end of the environmental tailpipe, with power-plant emissions from nearby states blowing across its border.

CAIR would have allowed New Jersey to discount pollution from other states when calculating whether it had met the standards.

But the rule was challenged and eventually shredded by the court.

Two things that Jackson will not have to deal with are a pair of midnight rules offered recently by the Bush administration. One would have made it easier to locate industrial plants near a national park and the other would have allowed coal-fired power plants to produce more pollution without installing new controls.

The EPA dropped those rules this week after it became clear they would not be approved at least 60 days before President Bush's departure, enabling Barack Obama to quash them when he takes office.

Claussen, who was at the EPA from 1973 to 1992, is heartened by the fact that Jackson is a conciliator. "There's a lot of talent at EPA and a lot of people who have thought long and hard about the issues," she said. "I don't think the EPA has had a good listener for a while."

Contact staff writer Sandy Bauers at 215-854-5147 or sbauers@phillynews.com.