[V]ermont Agriculture Secretary Chuck Ross this week proposed the toughest regulations yet on farmers who contribute to water pollution.

The agency wants authorization to remove animals from overcrowded farms where water quality is at risk from manure runoff, Ross told the House Fish, Wildlife and Water Resources Committee on Wednesday.

Just last year water quality advocates doubted Gov. Peter Shumlin’s commitment to the clean-up, but during the inaugural address earlier this month, he made it a centerpiece of his third-term agenda.

Ross reiterated the administration’s commitment to hold polluters responsible.

“This is one of the accountability pieces,” he told the committee.

The state is required under federal law to reduce the amount of phosphorus pollution into Lake Champlain. Nutrient runoff from farms, forests and developed land is responsible for toxic summer algae blooms that occur in sections of the lake.

The state presented a plan to the Environmental Protection Agency in May outlining how it would achieve the required phosphorus reductions. Though the plan still comes up short in certain sections of the lake — Missisquoi and South Lake bays — the EPA expects lawmakers to  authorize the necessary tools for the state to implement its plan, including the resources and authority to back it up.

Before the state can implement the stricter protocol, the agency must seek authorization from lawmakers to carry it out. Aside from the authority to remove animals from certain farms, the agency wants the power to issue civil penalties and impose pollution control measures.

According David Mears, commissioner of the Department of Environmental Conservation, these are some of the gaps that have hampered the agency’s authority to regulate farms. He said the enforcement penalties must be steep enough to discourage farmers to polluting the water.

“I think that these proposals are a significant shift,” Mears said.

State law says the Agency of Agriculture must provide farmers with financial assistance if it requires additional pollution control measures on farms, known as best management practices. Lake advocates have long said this is an impediment to the state’s ability to address agricultural pollution. The agency says, in practice, it has required best management practices without providing financial assistance.

Ross said the agency will no longer “recommend” new practices, but “require” them. He said this will expedite enforcement of water quality violations.

“We’re asking the farm business community to comply with the water quality rules of the state of Vermont like we are asking other businesses,” Ross said. “There are times, whether a non-farm business or a farm business, it may just not be the place where they can comply.”

“Because you were not able to run your businesses well enough to prevent yourself from polluting the waters of the state does not allow you to continue to pollute the waters in the state,” Ross said.

The state does have some federal grant money to help farmers make improvements. The state scored two competitive grants from the U.S. Department of Agriculture, which will provide funding to farmers who plant cover crops and fence out livestock from streams, among other purposes. Much of this money is funneled through the Natural Resources Conservation Service, or NRCS, and is available to farmers specifically for water quality improvements.

“But in the event that they don’t want to apply for those resources or if for some reason they weren’t available, then the farmer would be required to comply with the AAPs,” Ross said. “The alternative is to say that they may continue to pollute. And that is not acceptable.”

The agricultural community, which contributes the largest share of phosphorus pollution into Lake Champlain — 40 percent, and as high as 90 percent in Port Henry, N.Y., according to the EPA  — are now being asked to pitch in. The state wants farmers to follow water quality laws, known as accepted agricultural practices, or AAPs, and raising the stakes for those who do not.

Under the state’s proposed plan, small farmers will be required to certify that they are following the accepted agricultural practices. The state currently does not define what qualifies as a small farm. There are 169 medium and large farms in the state, according to the agency. In 2013, there were 7,300 possible farm operations, according to the U.S. Department of Agriculture.

The farming community is largely supportive of addressing water pollution, but many of the small farms that will be required to obtain certification that they are following water quality rules, are looking for some financial assistance. However, Ross said there may be times when following the AAPs will be a “true burden for them.”

Mark and Amanda St. Pierre started Pleasant Valley Farms in Richford in 1998. They milk 2,200 cows, plant 6,000 acres of crops, and have 75,000 maple tree taps. The farm is defined as large under state law.

Amanda St. Pierre said she and other farmers support the changes they are being asked to make to improve water quality. She said many farmers are “ready to do our part.”

She said the farm has made water quality improvements, such as building a lined manure pit, vegetative buffers between waterways, grass filter strips and a nutrient management plan, totaling $3.5 million. The St. Pierres also paid about $100,000 for filling wetlands prior to 2002, according to the EPA.

But for others, especially small farms whose profits are tied to the price of milk, the changes will not be so easy.

“My concern is that this has been costly for us,” she said. “I don’t think that the wide, sweeping (rules) and the quick response that we need to show EPA can be done without having some funding in place.”

Making matters worse, she said it can take years before funding arrives.

“A manure pit application, that is 12-to-18 months down the road,” she said. “That’s just to get evaluated — and you don’t even know if you’re approved at that point.”

The Vermont Agency of Agriculture’s proposal expands the scope of accepted agricultural practices under the law. The new practices include mandatory vegetative buffers, a prohibition on manure stacking and the exclusion of livestock from waterways.

Kim Greenwood, a water scientist with the Vermont Natural Resources Council, said the agency appears to be taking a positive stance on water quality that is different. However, she said many of the AAPs set a low bar, and could be enhanced. For example, she said there should be regulations on tile drainage.

The agency will report back to lawmakers on Jan. 15, 2017, with a study on tile drainage, which are pipes places under fields to drain away pools of water. Water quality advocates say the process sends pollution directly into larger water bodies.

The Agency of Agriculture is proposing to raise $1.2 million through an increase in the fertilizer fee from 25 cents per ton to $30 per ton. It will allocate $700,000 to hiring seven new staff and the remainder will go toward assistance to help farmers comply with the regulations.

By law, the state can only require farmers to change practices in ways that are practical and cost effective to implement.

“We can’t just start requiring massive infrastructure changes on all farmers if they’re not proactive and cost effective to implement. So there is a balance on that side that we have to consider that’s already in law,” said Jim Leland, the director of the agriculture resource management and environmental stewardship division at the agency.