About 10 scientists came to that conclusion after crunching fisheries and meteorological data, which the federal government began collecting in the late 1990s.
Their findings, originally presented to the judicial inquiry examining the historically low sockeye returns, have now been published in three papers in the journal Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science.
The publication comes before B.C. Supreme Court Justice Bruce Cohen is expected to present his findings into the issue in September.
"If you've got these years where oceanic conditions are unfavourable to food production you're really going to have trouble with the stocks," said Richard Thomson, a Fisheries Department oceanographer and a study co-author.
In 2009, only about one-tenth of the expected 10 million sockeye returned to the watershed, sparking the federally appointed Cohen commission to examine what caused the 2009 collapse of the Fraser River sockeye.
Numerous theories on why the sharp decline resulted were presented at the 21-month inquiry that wrapped up last November in Vancouver.
Thomson said scientists in the study he was involved in concluded that an "extraordinary event" was taking place in the Straight of Georgia, the body of water running between Vancouver Island and the B.C. mainland.
He said that when scientists began to notice there wasn't enough food in the stomachs of salmon, and there were fewer and smaller herring than usual, researchers formed an interdisciplinary team to tackle the issue.
"This team came together to try to understand how the physical environment could be affecting the fishery. And, you know, the herring was sort of a clincher, the fact that the herring were so stressed, and they're a food source for many of the fisheries."
Scientists focused on three related issues in an effort to understand what was going on.
Dave Preikshot, a fisheries scientist, and his four co-authors studied how long juvenile sockeye salmon were spending in the Strait of Georgia before heading out into the ocean.
"It appears to be at least 31 [days][ and it could be as long as, I think, 52 [days] is the upper limit there," he said.
Fisheries scientists in the 1950s and 1960s inferred that sockeye salmon didn't stay in the strait but migrated through it without lingering, Preikshot said.
In the 1990s, scientists suggested juvenile sockeye salmon were in the strait from 20 to 30 days, he said.
Establishing the amount of time the young salmon spend there is important because fisheries scientists believe the majority of fish die early in life, Preikshot said.
"If that is true, the longer they are in the Strait of Georgia, the more likely it is that significant things determining their return migrating population also occur in the Strait of Georgia," he said.
Retired biologist Dick Beamish, who is also an emeritus scientist with the Department of Fisheries and Oceans, tackled the issue of poor survival rate of sockeye salmon.
He found that while the Fraser River produced about 454 million juvenile sockeye salmon in 2007, only about 1.4 million returned in 2009.
"We think 2007 represented an extremely poor year for food production at the time those fish would either be entering the Strait of Georgia, or in the case of herring when the larval herring would first start feeding," Beamish said.
According to his paper, a survey fishery in 2007 noted a lack of juvenile sockeye salmon in the strait and the small size of sockeye that were caught.
Other kinds of salmon affected
The paper says coho and chinook salmon in the strait at the time were also smaller than in previous surveys. A high percentage of them also had empty stomachs.
A common diet item for juvenile chinook and coho salmon, herring were absent from chinook samples and greatly reduced in coho salmon, the paper adds.
"We interpret this to indicate that young-of-the-year Pacific herring were mostly dead by July 2007," states the paper.
"A most likely explanation for such a basin scale event would be a collapse of the plankton in the Strait of Georgia that are normally consumed by larval and juvenile Pacific herring."
In the third paper, Thomson and his five co-authors, including Beamish, argued unfavourable wind and freshwater run-off conditions were behind the low food production in 2007 and the poor survival rates.
Thomson said data collected at the time found massive amounts of fresh water entering the strait, and the wind, which flushes out the fresh water, wasn't strong enough and blowing in the wrong direction.
As a result, he said, the surface layer of the strait became highly stratified, creating a shallow cap that was too shallow for good plankton growth.
"We had all these ingredients coming together that was limiting, we think, the amount of plankton growth in the upper layer," Beamish said. "So all of the fish stocks had relatively poor food supply because of this structural change in the physical environment in the strait."
Thomson said the conditions occurred at a critical time, when juvenile sockeye salmon would be entering the strait.
"We think that first year is absolutely critical to their survival because that determines how big and strong these fish are going to be to be able to handle conditions out in the open ocean."
Fish migrating to the ocean would have then faced some similar conditions in Hecate Strait, Thomson said.
"Now these poor little buggers, not enough food, scrawny, they head out into the ocean. Now they've got to survive out in the ocean for two years. They're not big enough. They don't have enough reserves. Maybe that's where we lost them."