EDMONDS — Taking in the view from the pier on the city’s waterfront, it’s hard to sense anything could be wrong with Puget Sound.

The water is clear. It’s a popular place for people to cast their fishing lines or to toss metal-mesh crab pots into the water. Seals occasionally bob up among the rows of boats in the nearby marina. In winter, rafts of goldeneye ducks float on the waves near the ferry dock.

For all this, Puget Sound, with 2,500 miles of shoreline, isn’t nearly as healthy as it looks. And that’s one of the biggest challenges facing the Puget Sound Partnership, the state organization charged with improving the Sound’s health.

“It’s hard to hold in your mind the magnificence of this region, this geographer’s delight, the Salish Sea, and understand it’s not supporting life like it needs to,” said Martha Kongsgaard, chairwoman of the partnership’s leadership council.

“The rate at which we’re damaging the Sound still exceeds the rate of recovery,” Kongsgaard said. “We’re still polluting with stormwater runoff and still destroying habitat more than we’re restoring it. It’s really death by 1,000 cuts.”

The Puget Sound Partnership was launched by former Gov. Chris Gregoire, who appointed Bill Ruckelshaus, former head of the federal Environmental Protection Agency, as the first chairman. Kongsgaard now has that job.

The partnership was created to oversee and coordinate regional plans and projects to restore Puget Sound, and it serves as a clearinghouse for information.

“We coordinate, connect and mobilize resources,” Kongsgaard said. “It’s our job to figure out what to do when, and by whom, and to figure out if we’re using our money for the highest and best use.” The agency holds meetings regularly at locations around the Sound. The Science Panel, for example, held a routine meeting last week in Edmonds.

The Puget Sound Partnership’s challenge is seen in part by the decline in resident orca whales, the creature so associated with the region that its likeness is found on everything from coffee mugs to sweatshirts. They once numbered about 120, but the population has recently dropped to about 77, Kongsgaard said.

And salmon, whose near-miraculous migratory life cycle is celebrated each year, still are threatened, especially as they travel down streams that flow through urban neighborhoods.

The orcas need a lot of Chinook salmon — about 300 pounds a day — to survive, Kongsgaard said. “The food source is really a big problem,” she said. “They eat the fish and they have a lot of toxins.”

Steps are being taken throughout the Puget Sound region to try to stem the effects of urbanization, including 24 restoration projects that are planned, under way or completed in or near the Snohomish River estuary.

One of them, the 400-acre Qwuloolt Estuary project in Marysville, is one of the largest marsh restoration projects in the state. On Smith Island near the mouth of the Snohomish River, work is expected to begin next year on restoring 374 acres of marshland, said Heather Cole, an ecosystem recovery coordinator for the partnership.

Those are among the steps taken to meet a goal set a decade ago: improve 1,237 acres of estuary habitat in the Snohomish River Delta to increase the runs of bull trout, coho and Chinook salmon.

One of the biggest threats to the Sound’s health comes from the by-products of urban and suburban growth. Water from roofs, lawns, sidewalks and roads carry toxins. Those millions of individual sources are called non-point pollution, meaning they do not come from major industrial sources.

“Stormwater is a huge problem,” said Bruce Wulkan, senior policy advisor at the partnership on stormwater issues. Shellfish growing areas and beaches have been closed due to bacteria from stormwater runoff.

Stormwater pollutants contaminate sediment, are taken up by fish and work their way up the food chain. The result is that Puget Sound orcas are among the most contaminated marine mammals on the planet, Wulkan said. Although healthy salmon ready to spawn enter urban creeks, within hours they’re badly harmed and often dying before they get a chance to spawn, he said.

A five-year, $20 million U.S.-Canadian project is under way to try to find why so many salmon coming out of the region’s rivers die before they reach marine waters, Kongsgaard said.

No one knows exactly what is killing the salmon, at rates exceeding 80 percent, Wulkan said. “But they do know it’s stormwater. They’re guessing it’s a mix of contaminants.”

So there has been a lot of attention paid to cleaning up stormwater before it hits the Sound. The Legislature allocated $100 million to address stormwater problems statewide. Snohomish County and 14 area cities were able to get $50,000 grants for stormwater-related projects.

In his new two-year budget, Gov. Jay Inslee has proposed spending an estimated $700 million on Puget Sound recovery, with the two biggest chunks of money going for salmon projects and land acquisition and restoration.

Individual citizens need to play a role, too, Kongsgaard said. They can help by taking steps such as picking up and disposing of dog waste or repairing septic systems to reduce the amount of bacteria streaming into the Sound. Reducing or eliminating the use of lawn fertilizers and fixing motor oil leaks also can help.

“We individually are creating the problem,” Kongsgaard said. “But we’re the same people that can solve it. We can all agree that we love Puget Sound. It’s our back yard. You don’t have to be a card-carrying environmentalist to care about it.”

Sharon Salyer: 425-339-3486; salyer@heraldnet.com.