In coastal waters around the nation, harmful algae blooms are on the rise, oxygen levels are on the decline and seagrass beds have been rapidly disappearing. Valuable habitats are fragmented, degraded or vanishing—coastal Louisiana alone is losing roughly 25 square miles of wetlands a year.

Some fish stocks that once seemed inexhaustible are now in short supply—more than a quarter of the world’s fish stocks suffer from overharvesting—and many valued marine species are near extinction.

And more problems are on the way. Although U.S. coastal counties comprise only 17 percent of the nation’s land, they hold 53 percent of the population, and another 3,500 people are moving in every day, adding more strains to already stressed coastal and ocean ecosystems.

“Our oceans and coasts are in trouble,” said retired Admiral James Watkins, chair of the U.S. Commission on Ocean Policy. But despite the long list of woes, Watkins said all is not lost. The commission’s report, released Sept. 20, proposes sweeping changes in the way the nation’s oceans and coastal waters are managed, all the way from the office of the president to the local watershed.

“We as a nation have a historic opportunity to make a positive and lasting change in the way we manage them before it is too late,” Watkins said.

The 16-member commission, which was appointed by the president, conducted the first comprehensive review of the nation’s ocean policy in 35 years, and its 610-page report, with 212 specific recommendations, would transform a haphazard, and often ineffective, mix of bureaucracies and programs into a functional system that protects coastal and marine ecosystems.

The recommendations, if implemented by Congress and the president, would deal with a range of issues affecting the Chesapeake Bay, from the introduction of nonnative species to improved targeting of federal programs that curb pollution, especially runoff.

The report called for better decision-making at all levels of government, and emphasizes the need to focus on entire watersheds, not just areas bordering the coast. It calls for stepped-up investments in science to help improve decision-making, and a national commitment to “lifelong” ocean education to create an informed, and caring, public.

Today, 11 of 15 cabinet level departments and four independent agencies play some role in managing oceans and coastal areas. They, in turn, deal with state, local, tribal and territorial governments “in sometimes haphazard ways.” Sometimes, multiple agencies overlap in their responsibilities, while there is a void in federal oversight on other issues.

Establishing an offshore aquaculture facility, the commission’s report said, requires consultation with five federal agencies. But when it comes to introducing a nonnative oyster in the Chesapeake Bay, the report said, it’s unclear what federal agencies—if any—have a say in the decision.

To guide ocean policy, the commission recommended that Congress establish a National Ocean Council within the Office of the President which would be chaired by an assistant to the president. The council would include the heads of all departments and agencies that deal with ocean issues, and it would get advice from advisory panels consisting of scientists, state and local government officials and stakeholder groups.

In addition, the commission called for a network of regional councils—similar to the Bay Program—that would bring together state and federal agencies to voluntarily deal with regional and watershed issues affecting coastal and offshore waters. In fact, the report cited the Bay Program partnership as a “significant initiative by federal agencies, state and local governments, nongovernmental organizations, and other stakeholders to address the region’s water quality and living resource problems.”

At the federal level, the commission calls for strengthening the National Oceanic and Atmospheric Administration—which already contains the National Marine Fisheries Service and the National Ocean Service—to be the nation’s primary ocean agency.

Ocean and coastal programs in other departments would be reviewed with an eye toward consolidation where possible. For example, the report suggested that the EPA’s National Estuaries Program, which helps localities around the nation develop cooperative cleanup strategies, should be moved to NOAA. It does not specifically say whether the Chesapeake Bay Program, also administered by the EPA, should be moved.

The commission would beef up NOAA’s Coastal Zone Management Program, which provides grants to states to develop and implement plans to address coastal issues of local concern. The report said the program should get more money, and that NOAA should ensure that plans are more consistent from state to state and are written to get measurable results.

The report calls for earmarking up to $4 billion of the $5 billion collected annually in offshore oil and gas drilling royalties for coastal and ocean programs. That would go for such things as stepped-up research and monitoring, education, and helping state governments and local communities to develop better management plans.

But that money is unlikely to provide much help in funding the costly Bay cleanup. The report specifically stated that big-ticket restoration efforts such as the Chesapeake Bay, the Everglades and coastal wetland restoration in Louisiana would need other funding sources.

The report recognizes that the No. 1 problem facing the Bay—nutrient pollution—is also a major threat to other coastal waters. It said the reduction of nutrient runoff from coastal watersheds should become a “national goal” with measurable objectives set by the National Ocean Council.

Federal agencies need to improve coordination to curb runoff, the report said. In particular, it said the U.S. Department of Agriculture should do a better job of aligning its conservation programs with EPA and NOAA programs aimed at reducing coastal pollution. It said nutrients and chemicals from animal feeding operations should be targeted for more research and control efforts.

In addition, the report said the EPA should require all wastewater treatment plants affecting coastal waters to upgrade with nutrient control technology, and ensure that new stormwater regulations are implemented. It said the agency should target grants and other assistance to deal with aging, leaking sewer systems. It also said the government needs to do a better job of reducing air pollution, which literally rains nutrients, as well as toxins, on coastal waters.

The report called for stepped-up efforts to combat the growing problem of invasions by nonnative species, including enforceable ballast water treatment standards for oceangoing ships. Ships routinely suck in water at one port as ballast, then discharge it—along with any organisms it contains—at its destination.

More than 2 million gallons of ballast water are released every hour in U.S. waters, and many of the 500 nonnative species now inhabiting coastal waters are thought to have arrived thorough ship ballast.

Many have had devastating effects. The oyster disease MSX, which originated in Asia, is partly to blame for dramatic reductions in the Bay’s oyster population. Zebra mussels caused between $750 million and $1 billion in natural resource and infrastructure damage to the Great Lakes from 1989 and 2000.

Because prevention cannot be entirely effective, the report calls for monitoring to catch invaders early, and the development of rapid response programs to eradicate them when possible.

The report took note of the current debate within the Bay region about whether a foreign oyster, Crassostrea ariakensis, should be introduced in the Chesapeake, saying there was a “noticeable gap in regulatory authority” over such introductions. State and federal agencies have differed over who has the ultimate authority over an intentional introduction, and they also differ over how much research is needed before a decision is made.

The report said clearer policies are needed for such proposals, and that the proposed National Ocean Council should “clarify lines of authority” over intentional introductions and develop guidelines about how risk assessments for such introductions should be done.

Critical coastal habitats that support fish and other marine species are stressed by lost and degraded habitats as coastal populations grow. The report called for a national strategy, with goals and priorities, to restore wetlands, seagrass beds and other critical habitats.

Noting that natural hazards such as floods and hurricanes cost at least $50 billion a year, the report said federal agencies need to change policies that encourage inappropriate development in hazard-prone areas, and it called for universal state and local hazards mitigation planning.

The report would revamp the way fisheries are managed in federal waters—those more than three miles offshore—to be more protective of fish stocks and their habitats. It said the number of people permitted to participate in those fisheries should be limited to prevent the “race for the fish” that occurs when too many commercial fishermen are competing for too few fish.

What happens with those recommendations remains to be seen. Although some bills that seek to implement the recommendations have been introduced in Congress, no action is expected until next year. The report itself notes that legislation aimed at revamping federal agency jurisdiction over ocean policy has a long history of failing.

But the report adds weight to a growing call for action. Last year, an independent panel funded by the Pew Foundation, with its own team of policy makers, made a similar set of recommendations.

Donald Boesch, president of the University of Maryland’s Center for Environmental Science and a member of a scientific panel advising the commission, said the each new report builds support which could translate into action, although he doubted it would result in significantly increased budgets.

“The significance is in the big message,” he said. “For a whole variety of reasons we have some serious problems with the health of our national ocean waters around the U.S., and that to deal with it is going to require some different approaches that will challenge government to work across boundaries.”

But others noted that Congress already appears to be going in the wrong direction, as several speakers at a forum on the report, sponsored by the Virginia Institute of Marine Science, pointed out that federal funding for ocean and fisheries programs is being cut, not increased.

In fact, spending bills for next year would cut funding for one of the commission’s high priority items—NOAA’s Coastal Zone Management Program and its efforts for dealing with polluted runoff.

“The economic value of our coastal oceans is in the trillions of dollars, and yet our investments are only in the millions,” said Laura McKay, who oversees Virginia’s Coastal Resources Management Program.