When congressional Republicans cut the Environmental Protection Agency’s budget 16 percent as part of a deal with President Obama in April to keep the government running, they hailed it as a blow to a federal bureaucracy that had overreached in its size and ambition.

But now that the agency has detailed how it is making the $1.6 billion cut for fiscal 2011, the reality is somewhat different. Because the EPA passes the vast majority of its money through to the states, it has meant that these governments — not Washington — are taking the biggest hits. Already constrained financially at home, state officials have millions of dollars less to enforce the nation’s air- and water-quality laws, fund critical capital improvements and help communities comply with new, more stringent pollution controls imposed by the federal government.

Indian Head, Md., won’t get the nearly $1 million it has requested to improve sewer lines and rehabilitate manhole covers. Wyandotte County, Kan., has suspended its hazardous-waste public awareness programs. And Virginia will scale back the studies it is conducting to evaluate nitrogen runoff into the Chesapeake Bay.

“The federal government and state grants are both shrinking while our demands are increasing exponentially,” said Andrew Ginsburg, air quality division administrator at Oregon’s Department of Environmental Quality. “We’re definitely feeling the crunch here.”

The EPA was a central target for Republicans during the spring budget battle, as they tried to curtail its authority to curb greenhouse gases, mercury and other pollutants. Although lawmakers failed to secure those provisions, they limited the agency’s activities through budget cuts.

But as lawmakers and local officials assess the impact of those cuts, few seem pleased with the outcome.

“We made some tough choices in there,” EPA Deputy Administrator Robert Perciasepe said in an interview. “We’re very close to the edge where you start to erode the capacity of the agency.”

S. William Becker, executive director of the National Association of Clean Air Agencies, said lawmakers didn’t realize that targeting EPA’s budget meant “that they’re cutting jobs at the state and local level. If they knew that, maybe Congress might have acted differently.”

Key Republicans say the cuts have failed to reshape the agency the way they had envisioned.

“By stepping into the process in the middle of the year, we weren’t able to provide the kind of details you can when you’re doing an appropriations bill from the outset,” said Rep. Bob Goodlatte (Va.), vice chairman of the House Agriculture Committee and a frequent EPA critic. “The EPA made a lot more decisions in how they made the cut, and I certainly don’t agree with how they made the cut or spent the money.”

In fact, many of the funding decisions the EPA made this year were based on a mandatory formula, since $1 billion of the overall reduction affected just two programs helping underwrite clean-water and drinking-water projects.

“This is one of the problems with cutting EPA’s budget. You look at a lot of their programs and they are pass-through programs,” said House Interior and Environment Appropriations Subcommittee Chairman Mike Simpson (R-Idaho), referring to programs whose funds flow directly from the agency to the states. “When you’re reducing the budget, those programs are going to go down substantially.”

Agency officials were able to protect some of the administration’s top priorities, such as providing more money to clean up the Chesapeake Bay. It provided an additional $4.3 million to the Chesapeake Bay program while cutting every other regional cleanup, including in the Great Lakes and Puget Sound. It allotted nearly $4.6 million to research of endocrine disrupters, chemicals that have entered American waterways and pose a potential public health threat.

“We’re using the funds to proceed on some of the key things we’re trying to do,” Perciasepe said, adding that the EPA has identified 2011 as a critical year for finalizing Chesapeake Bay cleanup plans.

But Republicans succeeded in blocking more than $8.5 million the EPA would have provided to help states cope with new rules limiting greenhouse gas emissions from power plants and refineries.

Simpson said he and other Republicans are going to look at whether they can target reductions at the EPA headquarters for the next fiscal year, perhaps by limiting the number of full-time-equivalent positions at the agency. By doing so, he said, it might curb the EPA’s efforts to impose mandatory limits on greenhouse gases and other forms of pollution: “Many of us believe the EPA has gone beyond what Congress has wanted or authorized it to do,” he said.

In the meantime, state and local officials who oversee the nation’s air and water quality — most of whom were already dealing with smaller state budgets — are struggling to cope with the sudden dip in federal funding.

Walter Gills, program manager for Virginia’s clean-water revolving loan fund, said the state learned so late it was losing $10 million for low-interest loans that it had to find money elsewhere and will cut the program much deeper next year.

“We just couldn’t pull the plug,” Gills said. He added that since EPA’s budget will probably shrink again in the next appropriations cycle, “it could actually be a double whammy next year.”

In Oregon, Ginsburg said, his agency has postponed hiring an environmental engineer and is reducing its pollution monitoring work.

Just as his agency is being asked by the federal government to enforce new smog, soot and greenhouse gas rules, it is facing a cut in federal assistance to execute the task.

“We’re just a microcosm of what’s going on around the country. The same thing is going on in every state,” Ginsburg said. “It’s just adding up to a crisis mode.”