We’ve learned where they go in winter, confirmed that they eat chinook salmon more than anything else, and we now try to keep noisy boats away from them. But even after 10 years of research, the number of southern-resident killer whales in Puget Sound is still in decline.

It would be so much easier if the whales had faced just one problem.

In the decade since Puget Sound’s southern-resident killer whales were protected under the Endangered Species Act (ESA), scientists have figured out where orcas go in winter. They’ve learned these whales can tell a chinook from a sockeye by using sonar to detect small differences in each fish’s swim bladder. And researchers have documented the many ways these majestic mammals shift behavior in response to propeller and engine noise from boats.

Yet despite the vast rise in knowledge since killer whales were listed as endangered in 2005, the region’s orca population — already a fraction of what it was in the 1960s — still is not growing, according to a new synopsis of research on the cetaceans by the National Oceanic and Atmospheric Administration (NOAA).

Scientists are “trying to understand … why the whales haven’t increased more than they have,” said Mike Ford, with the conservation biology program at NOAA’s Northwest Fisheries Science Center.

In one sense, they already know: An explosion in whale science reveals that orcas face complex and overlapping threats that tend to compound one another.

“Part of what I hoped at the beginning was that it would be mostly one thing that was wrong,” said Brad Hanson, a whale expert with the fisheries center. “But they all appear to be intertwined.”

In the early 1960s, Puget Sound’s killer whales numbered 140 — and some scientists suspect that a century before there might have been 200 or more. By the early 1970s, after entrepreneurs began capturing orcas for sale to marine parks, the population had plummeted to just 71. Capture was outlawed a few years later, and orca populations climbed to 99 in the mid-1990s.

As of last year, only 82 remain.

Three main factors appear to contribute to their decline — a lack of food, the buildup of pollutants in their bodies and disturbance by marine vessels. Still, understanding the subtle ways these and other marine-world changes interact only seems to get more complicated.

These whales, it turn out, may eat lingcod and halibut but key in mostly on chinook — which face severe threats of their own. The region has spent tens of millions of dollars to try and improve this other ESA-protected species, though a scathing 2011 report suggested too little progress was being made.

In addition, noise from boats, which is on the rise, prompts orcas to speed up, work harder, slap their tails more and hunt less — which means they may burn more calories just as they’re getting less food.

New rules require boaters and whale-watching vessels to stay 200 yards from whales, but state enforcement has shown the response has been decidedly mixed, said Lynne Barre, head of protected resources for NOAA’s Seattle office.

Meanwhile, these long-lived mammals already are among the most polluted animals on Earth, with toxins accumulating in their fat over decades. When whales get hungry contaminants may well mobilize in their system, potentially affecting their health and reproduction.

But while efforts to clean up Puget Sound’s legacy pollutants are under way the whales’ position at the top of the food chain means they still collect out-of-use pesticides like DDT and banned chemical like PCBs. With other pollutants, such as flame retardants, only now being recognized, those will probably survive in killer whales for many decades longer.

And all these issues are more complex than they first appear.

For example, some orca pods are more heavily burdened by DDT than others, most likely because they rely on fish from rivers in Central or Northern California, which are more heavily influenced by agriculture.

Whales feeding on fish from the north, in more urbanized environments like Seattle and Vancouver, carry a bigger load of PCBs.

“They pick up contaminants from where they’re going,” Ford said. “L and K pods tend to pick up California-type contaminants, compared to J pod, which doesn’t, and that’s consistent with their distribution.”

And these orcas are declining just as other Northwest marine mammals relying on fish — including seals, sea lions, even other killer whale populations — actually are on the rise.

The northern-resident killer-whale population has tripled to nearly 300 since the 1960s. Northern and southern whales share similar diets. But Puget Sound’s southern whales are distributed from California to Alaska, while the northern whales travel mostly between northern Washington and Alaska.

The growth of the northern population may even be helping keep the southern resident populations down.

“It’s possible that some of those increases influence the rate at which southern resident populations grow,” Ford said.

For starters, northern whales may have a food advantage.

“One thing we’re considering is that the northern-resident population may have first crack at the best salmon stocks,” Hanson said. “A lot of the West Coast fish, they come out of the rivers, they turn right and head north.”

Other problems make life hard for southern residents.

Two of the three southern- resident pods have a shortage of young females. This population already gives birth to fewer young less often than northern north residents, and “it doesn’t take much to tip the balance the wrong way,” Hanson said.

J, K and L pods also often are born to parents within their pod, a form of inbreeding that could reduce genetic diversity and make whales susceptible to disease or genetic disorders.

And there’s no shortage of other mysteries.

When killer whales die, they rarely wash up on the beach for researchers to find and study, Barre said. Instead, they just disappear and scientists never know what caused them to die.

And much of their behavior remains unpredictable.

“Why do they sometimes decide to turn out toward the ocean and stay there for two weeks?” he asked.