Part One: Why are the killer whales disappearing?

SEATTLE -- This past summer, seven Puget Sound killer whales went missing and are presumed dead in what would be the largest decline in the local Orca population in a decade.

There were once hundreds of southern resident Orcas swimming in the waters of Puget Sound and now there are fewer than 90. Scientists say many of those are starving.

Researchers say there are three things behind this decline, fewer Chinook salmon — their primary food source, pollution and — us.

The Southern Resident Killer Whale is one of nature's most powerful and majestic animals.  From the islands to the streets of Seattle, their image is everywhere.

Orcas are the top level predator in the sea.  Adult males weigh up to nine tons and can swim 30 miles per hour.  They live in every ocean, all over the world.  Some are known as transients, regularly migrating from one region to another.  Others are residents, living primarily in one place year-round.  The Pacific Northwest is home to three pods of southern resident orcas, J, K and L.

For the average person, it can be difficult to tell these whales apart, but not for Ken Balcomb with the Center for Whale Research in Friday Harbor.

"The males have a tall dorsal fin.  The females have a smaller fin and also a saddle pattern," says Balcomb.

For the last 35 years, Balcomb and his team have been tracking our resident pods of Southern Resident Killer Whales.  They give each animal a name based on which pod it belongs to.  The latest news isn't good.

"Right now we have four missing.  K11, L73, L74 and J33 are all adult animals.  This is somewhat concerning," says Balcomb.

Three of those missing whales are breeding age males which are critical to keeping the population going.  That's a serious issue because while there were once hundreds of southern resident orcas swimming the waters of Puget Sound, now there are fewer than 90.  Only about 25 of those are of breeding age and experts say many of those are starving.

"When you get a depression behind the skull you sort of have this valley.  We call it a peanut head," says Balcomb.  "They rarely recover from that.  Usually when you see that much emaciation and loss of fat and blubber, they're beyond surviving.  They might last two weeks.”

“Did any of the four missing whales have that appearance?” asks Q13 FOX News reporter Dana Rebik.

“We're looking at that now, but yes, we saw hints of it," says Balcomb.

Scientists at the University of Washington have reached the same conclusion following a very different kind of research.  At the Center for Conservation Biology, a specially trained dog named Tucker sniffs out Orca poop near San Juan Island which is then collected and analyzed.

"You can tell the species, sex and DNA from the scat.  Also if the animal is stressed and if it’s getting enough food,” says UW professor Sam Wasser.

"We're seeing higher stress during times of low prey abundance and also lower nutrition and higher mortality," says PhD student Katherine Ayres.

"Does that prove they are starving?” asks Rebik.

“It does certainly suggest that's something to do with what's happening," says Ayres.

Starvation is one of three factors contributing to the diminishing Orca population here.  Chinook salmon are the Southern Resident Orcas primary food source.  While the Columbia River Basin was once teeming with millions of Chinook, the National Marine Fisheries Service estimates there are only around 30,000 left.

Number two is pollution.  Salmon are heavily contaminated with toxic residue from their environment.  The whales eat those fish and the pollutants are filtered out into their blubber.   Without enough to eat, those chemicals can affect their health.

"When you starve, you burn fat and dump toxins into the system and you whack your immune system.  That in turn shuts down critical hormonal pathways," says Wasser.

The third and most controversial threat to the Orcas’ survival comes from one of the most vibrant tourism industries in Washington.

"There is a growing body of scientific literature that's documenting the impacts boating can have on the whales" says Lynne Barre with NMFS.

Orcas are acoustic animals that use clicks, whistles and calls to communicate, define their environment and find food.  Their hearing is so sensitive they can communicate with other members of the pod across many miles of ocean, but when so many boats are in the water, their engine noise disrupts the process.

“We are mostly concerned about behavioral disturbance from boats and the sound the boats make and how that can inhibit the whales’ ability to find food," says Barre.

In 2005, Orcas were added to the Endangered Species list.  Those protections specifically prohibit, “…any act of pursuit, torment, or annoyance which has the potential to injure a marine mammal …in the wild; or has the potential to disturb a marine mammal…in the wild by causing disruption of behavioral patterns.."

Yet these creatures are relentlessly pursued from May to October by whale watching crews from the US  and Canada.  Their locations are reported by professional Orca spotters whose job it is to tell whale watch crews exactly where they are.

"With a lot of noise it would be like people with the lights off being in the dark, not being able to see what's around you or see who's next to you," says Barre.

Barre says motor noise from whale watch boats and other vessels constitutes enough of a threat to the orcas that the agency is drafting additional rules to keep them farther away from the animals as part of its Species Recovery Plan.

The question is will it be enough?  Every scientist we spoke to agreed unless something is done, and soon, these pods are headed for extinction.

"There's not only a chance it's almost a certainty," says Ken Balcomb.  "There goes our most charismatic marine mammal we have, gone."

There is some good news to report.  According to the Center for Whale Research, a calf was born in October.  The calf was named L116 and is the third baby born in L pod this year, but one of the three died after birth.

PART TWO: We go undercover on two whale watch boats . You will also hear from whale watch boat owners who deny their business is having a negative impact on the whales as our special series continues.