DECADES OF on-again, off-again attempts to clean up the Chesapeake Bay took a quantum leap last year when the federal government decided at last to crack the whip on pollutants that have turned parts of the estuary into a killing zone for plants, fish and crustaceans. The Environmental Protection Agency’s “pollution diet,” finalized in December, set tight limits on the levels of nitrogen, phosphorus and sediment that starve the bay of oxygen and turn swaths of it into a lifeless soup.

In mounting a full-court press to clean up the bay, the EPA made it a national test case, a fact not lost on agricultural and other polluters. Now farmers and home builders are pushing back, challenging the EPA in federal lawsuits that, if they succeed, would deal a major blow to hopes that the bay can be restored to any semblance of robust health. The lawsuits will determine the government’s ability to revive other pollution-damaged waters in the Gulf of Mexico, Puget Sound, the Great Lakes and elsewhere.

To their credit, Obama administration officials have promised to fight the lawsuits, which challenge the science and authority behind the EPA’s pollution limits. It’s critical that they do. Scientists who study the bay have seen encouraging signs of life in recent years, including a sharp rebound in the population of blue crabs and a revival of underwater grasses. But progress has been fragile. In other areas, including the decimated oyster population, there’s a long way to go.

That was apparent in June when a third of the bay, from Baltimore to the Potomac, was consumed by a gigantic “dead zone” of oxygen-starved water — the product of nutrients from fertilizer and other chemical runoff — that posed a deadly threat to marine life. Dead zones occur regularly in the bay; scientists say the unusually large one triggered by this year’s heavy spring rains does not signal a long-term trend. Still, it was a useful reminder of the threat posed by agriculture and home builders — the very interests challenging the EPA’s drive to restore the Chesapeake.

Much remains to be done in prodding industrial farms to adopt best practices to limit runoff; in upgrading sewage treatment plants with new technology; and in developing tighter standards to control storm water in both urban and suburban neighborhoods. And it will be expensive.

In Maryland, lawmakers are considering an increase in the so-called flush tax — a $2.50 monthly levy on all households, enacted in 2004, that has yielded tens of millions of dollars to modernize sewage treatment plants. In Virginia, which has not earmarked a specific tax for that purpose, the state may have to look for new revenue elsewhere to accelerate sewage plant upgrades.

The cleanup effort will impose billions of dollars of costs on all levels of government and on farms and industry. But those costs must be measured against the Chesapeake Bay’s critical economic importance to Virginia, Maryland, and other watershed states and against the even greater costs of continued inaction.