BOSTON - Gov. Deval Patrick's budget cuts could have been much worse for homeowners, farmers and others who benefit from the state's environmental programs.

Thanks to what is being called a unique innovation, more than half of the $38 million in program cuts won't be felt because of the governor's efforts to get agencies outside state government, such as the Massachusetts Water Resources Authority, to cover the cuts.

"I believe it's unprecedented," said Cyndi Roy, spokeswoman for the Office of Administration and Finance, which oversees spending and develops the annual budget.

"I think it's the first time everyone's stepped up and prevented us from having to go through with expanded 9C authority."

But the outside funding that will mitigate 9C cuts - named after the state law that allows the governor to make certain budget decisions without legislative approval - won't be available for the next budget cycle. If the budget deficit widens, the Office of Energy and Environmental Affairs may have to cut into critical programs and staff positions. Officials say they are already drawing up tighter budgets for fiscal year 2010.

"It's still too early to say if this round of 9Cs was enough," Roy said.

For now, many environmental departments have had new positions and programs eliminated.

"In general, the budget cuts in EEA agencies eliminate legislative earmarks and reduce new hires and keep previously budgeted positions unfilled," said Lisa Capone, a spokeswoman for the Office of Energy and Environmental Affairs.

In the Department of Agricultural Resources, which supports farming efforts statewide, cuts to administrative funding will shrink the budget by 10.2 percent and eliminate eight new positions.

The department also lost funding for the Agricultural Innovation Center, a new program that will provide technical and business development services to farmers. The program's $1.5 million original budget has been cut by one third.

Michael Rock, budget director for the agriculture department, said that while the program cost $3.2 million to establish in 2007, the department reduced the center's budget to $1.5 million in fiscal year 2008 and 2009. But the $500,000 in cuts comes from the account for grants and subsidies - not operational expenses. As a result, Rock said, the cuts will not affect the program too much.

The Department of Conservation and Recreation, which has the largest environmental budget, also has the largest share of the cuts. Some $8 million, or 8 percent of its $101.8 million budget, has been cut. But a closer look reveals that more than half of the cuts are to earmarks for such limited programs as statewide resource management and mounted park rangers.

"We are still reviewing the budget cuts and determining what to do," said Wendy Fox, spokeswoman for the agency. "We are still working to determine the impact of those cuts."

Fox also said the remaining cuts will come by eliminating travel expenses and not filling vacant positions. There will be no layoffs, she said. Most significantly, a $20 million cut in funds subsidizing water and sewer bills in the Boston metro area won't be felt at all. The Massachusetts Water Resources Authority, a quasi-governmental agency that oversees the water and sewer infrastructure for the area, is using its own funds to offset $15 million of the cuts.

A number of smaller water and sewer authorities will cover the other $5 million.

Though the MWRA operates independently from the state and raises its own revenue, the Legislature has appropriated money in recent years to keep water and sewer fees the authority charges at more affordable levels. But the subsidy is usually the first to be cut in lean years - which is what happened during the 2003 budget crisis when the Legislature eliminated $47 million in appropriations for the authority. The result was a 4 percent mid-year rate hike.

This time the authority is lending a hand. Ria Convery, a spokeswoman for the authority, said the savings will be made by cutting back on overtime for the agency's 1,200 employees, leaving non-essential positions vacant and hiring fewer contractors to help with in-house design work.

The authority also recently refinanced some of the $6 billion in debt from projects like the Boston Harbor cleanup, freeing up more funds. "We're going through every line item," she said. "We're pretty confident we're making up the shortfall."

But the ratepayers' reprieve may be temporary. An uncertain economic future may require more cuts and force the agency to raise rates next year.

"We're trying to construct a minimalist budget for next year in case more cuts have to be made," Convery said.

Roy, the Administration and Finance spokeswoman, echoed the pessimism.

"Things are not going to improve in this fiscal year," she said. "(Next year) we will be faced with very difficult choices."

This report was prepared for The Sun Chronicle by the Boston University Statehouse Program.