A federal judge on Friday upheld the EPA’s ability to impose a “pollution diet” on the Chesapeake Bay watershed, rejecting a challenge brought nearly three years ago by agricultural and development interests.

U.S. District Court Judge Sylvia Rambo said in her 99-page decision that the EPA acted within its authority under the Clean Water Act when it issued the Chesapeake Bay Total Maximum Daily Load in December 2010 after decades of previous efforts had failed to restore the estuary’s water quality.

“The ecological and economic importance of the Chesapeake Bay is well-documented,” she wrote. “As the largest estuary in the United States, the Chesapeake Bay is essential for the well-being of many living things.”

Yet despite “extensive efforts” to clean up its water, Rambo noted that “nutrient pollution and sedimentation remain a critical concern.”

The TMDL, or “pollution diet” established enforceable limits on the amount of nitrogen, phosphorus and sediment that can enter the Bay from its watershed each year. The EPA also required states to develop detailed plans showing how they would implement by 2025 all of the actions needed to achieve the steep — and likely expensive — pollution reductions needed to meet the Bay TMDL goal.

The EPA has issued or approved more than 40,000 TMDLs for other waterbodies across the nation, but the Chesapeake TMDL was the largest and most complex. It affects the Bay’s entire 64,000-square-mile watershed, and allows the EPA to impose a variety of penalties on states that fail to make adequate progress toward achieving nutrient and sediment reduction goals.

Nutrients and sediment and sediment cloud the Bay’s water, degrade habitats and contribute to oxygen-starved dead zones.

The American Farm Bureau Federation and Pennsylvania Farm Bureau filed suit to block the implementation of the TMDL just weeks after it was issued. They were later joined by a number of other agricultural trade organizations, as well as the National Homebuilders Association, all of whom worried the TMDL would result in expensive new regulations, and that it could set a precedent for other parts of the nation.

The EPA, in a statement, called the ruling “a victory for the 17 million people in the Bay watershed.”

A Farm Bureau spokeswoman told the Associated Press that it was “disappointed” but was reviewing the decision.

The plaintiffs had argued that the EPA overstepped its authority, and assumed responsibilities delegated to the states under the Clean Water Act.

But Rambo disagreed, saying the TMDL, whose pollution limits were largely developed in cooperation with the states in the watershed over a period of more than two years, was an example of “cooperative federalism, as envisioned by the [Clean Water Act].”

  “Indeed, considering the numerous complexities of regulating an interstate water body, EPA’s role is critical to coordinating the Bay Jurisdictions’ efforts to ensure pollution reduction,” Rambo wrote.

She also rejected other arguments made in the suit, including that the EPA used flawed computer models in developing the TMDL and that the agency had not allowed enough time for public comment before issuing the plan.

Environmental groups who sided with the EPA in the case hailed the decision, saying it removed any ambiguity about about the need to implement plans to clean up the Bay.

“This is a great day for clean water in the region, there could be no better outcome,” said William Baker, president of the Chesapeake Bay Foundation, which brought a suit that helped force the EPA to develop the TMDL.

“The court made it clear the agency is authorized to continue doing what is necessary to reduce pollution entering the Chesapeake Bay and protect the water that sustains people, wildlife and livelihoods,” said Larry Schweiger, president of the National Wildlife Federation.