SEATTLE >> Photographer Matt McDonald had lived on Puget Sound for years but had never seen a whale, so he was elated when he spotted a giant marine mammal just off Seattle’s waterfront one evening.

The excitement was short-lived. As McDonald tracked the whale in his camera’s viewfinder, a state ferry that dwarfed the animal came into the frame. The next morning he saw on the news that the humpback whale had died in the collision he witnessed.

“I still remember the moment of when they crossed paths and my heart just sinking like, ‘Oh my God, the ferry just ran over the whale,’” he recalled of the 2019 encounter. “I wish there was something I could have done.”

Now, five years later, there is.

The U.S. Coast Guard has launched a pilot program to alert ships of whale sightings in Washington state’s Salish Sea. The goal of the agency’s “cetacean desk” is to keep the marine mammals safe from boat strikes and reduce noise in the highly transited inland sea waters.

The program, which began official operations in December, comes at a time when visits by humpback whales and sea mammal-­hunting orcas increase as their populations rebound.

Fed by the Pacific Ocean, the Salish Sea is a maze of islands and canals that make up the inland waters between Washington state and British Columbia, including Puget Sound. Two groups of orcas — one that preys on salmon and the other on sea mammals — as well as baleen whales have cruised these waters since time immemorial and are now often visible from Seattle’s shoreline.

But these waters are now also home to major American and Canadian ports, and nearly 300,000 vessels crisscrossed the area in 2023, from commercial container ships to cruise ships to ferries, according to the Coast Guard. That doesn’t include private crafts.

John Calambokidis, senior biologist at the Cascadia Research Collective, said baleen whales, like humpbacks, are especially susceptible to ship collisions at night because they spend twice as much time near the surface then.

Earlier this week federal officials urged boat operators to be vigilant in Hawaii waters after a humpback whale calf appeared to have been struck off Maalaea Bay, Maui. Reports of an injured calf prompted an assessment by researchers from the Hawaiian Islands Humpback Whale National Marine Sanctuary and the Pacific Whale Foundation.

The sanctuary concluded that the calf — which exhibited limited ability to swim — was likely suffering from blunt force injuries due to a boat strike.

It’s a reminder for all on the ocean to “keep a sharp eye out” and “go slower” during humpback whale season, said Ed Lyman, the sanctuary’s natural resource specialist. In the vicinity of the whales, data strongly suggests the transit speed should be 15 knots or less.

Thousands of whales migrate from Alaska to the warmer waters of Hawaii each year to mate, give birth and nurse their calves. There are many mother-calf pairs currently in Maui waters, according to Lyman.

At least five other strike cases of whales have been reported so far, he said. Some, including another calf last week, bear visible injuries such as propeller scars.

The new whale desk in Salish Sea reduces the risk of collisions by combining sightings by mariners and civilians on whale-watching apps and data from underwater listening devices into an integrated system that will send out alerts to commercial vessels and regional ferries through a mobile app. The alerts will not go out to private or recreational boats.

“We’re focusing on empowering the ship operators with the situational awareness … so they’re able to slow down preemptively, perhaps give a little bit of a wider berth to an area with a recently reported whale,” said Lt. Commander Margaret Woodbridge, who is managing the whale desk.

The Salish Sea is an “incredible area that has a lot of a rich diversity of whale species here,” Woodbridge added. “And also a lot of economic activity on the waterways. And so we’re really trying to help both thrive.”

People who spot whales can download one of two apps that will feed into the Coast Guard’s Puget Sound Vessel Traffic Service. Mariners can use radio frequencies and a phone tip line when they spot whales. Participation in the program is voluntary for ships.

The whale desk is modeled to match the Canadian Coast Guard’s “Marine Mammal Desk.” Both American and Canadian desks are built on the backbone of the Whale Report Alert System, a program developed by Canadian-based Ocean Wise that incorporates sightings from the individuals apps and other sources, such as a private tracking information used by whale-watching boats.

The Salish Sea’s four-year pilot program, initially created for the well-being of endangered southern resident killer whales, is the culmination of years of work by wildlife advocates, the maritime industry and state and federal agencies. It was created after U.S. Sen. Maria Cantwell sponsored it in the 2022 Coast Guard Authorization Act.

“It’s really a bit of a watershed moment,” Kevin Bartoy, who has been chief sustainability officer for Washington state ferries for about a decade, said of the alert system.

“The amount of sightings now that we get on any given day is incredible. We can know essentially where a whale is at any time.”

But work is not done. The whale desk is mostly based on what people can see, leaving spotting the animals at night and in inclement weather much harder.

Bartoy said studies are underway in Canada and Washington to start testing land-based thermal cameras that could potentially spot whales at night by seeking their warmth in the waters as well as a more robust underwater listening — or hydrophone — system to pick up whale songs.