We met at the water’s edge at dusk. The evening was warm and the sky was clear—a nearly perfect early September evening for a paddle in the dark. At this time of year, roughly 75 miles north of San Francisco, at the mouth of the Russian River, when the moon has faded and the water temperatures and tides are just right, the water glows.

Our group of six had come to the small town of Jenner, along the Sonoma County coast, to experience the bioluminescence of the Russian River’s estuary. The conditions on the night of our visit, as luck would have it, were nearly perfect. The water extended to the horizon like polished glass. There was not a trace of wind and only the wispiest cloudlets hung over the typically fog-choked bay at the river’s terminus. Most importantly, the thin crescent of the waning moon would not rise until much later in the evening.

Kayaking the San Francisco Bay at dusk with Sea Trek.
Sam Huff, Director of Operations, Sea Trek, LLC

Our guide, a wiry man in his mid-60s named Keith Chandler, was optimistic. He said the calm conditions would make paddling a breeze. And if all the biological factors lined up, he said, the glowing microscopic organisms clustered along the water’s surface would create a marine lightshow we wouldn’t soon forget. The otherworldly glow is a natural phenomenon. But in a warming world it can also be a warning–a glimmering indicator of an ecosystem out of kilter.

Chandler, known to visitors as “Kayak Keith,” has worked with the Jenner-based WaterTreks for the last 5 years. He uses a handy one to ten scale to rate the glow. The best he’s seen here at the mouth of the Russian River, he says, was a nine. “It was incredible, but I want to leave some wiggle room. I don’t want to have to go to 11.” He expected the night of our visit to be good, but not necessarily spectacular.

“I think we’ll be at about a seven.”

After outfitting us with paddles and floatation devices, Chandler gave us a quick tutorial on how to safely maneuver our tandem sea kayaks through darkness. Suitably trained and equipped, we launched into the bay as the sun dropped below the horizon. My 17-year-old son and rowing companion, Owen, was seated at the front of the boat and gave an admonishing laugh as our vessel veered hard to the left. It took a few minutes to find our rhythm and coordinate our paddle strokes to make our boat move in a straight line. Once we’d gained control, we aimed for a beacon—a blue glowstick, which dangled from a string on Chandler’s back—fifty yards away across the water’s smooth surface.

Waiting for the night to fall on San Francisco Bay with Sea Trek. Sam Huff, Director of Operations, SeaTrek, LLC

We paused in the middle of the bay just as the silhouetted head of a harbor seal popped above the waterline. Chandler explained that the microorganisms responsible for the glow, called dinoflagellates, inhabit a thin layer in the top few inches of the water column. “They are motion activated,” Chandler said, smacking and swirling his oar on the water’s surface. Each stroke, he said, brings them to life.

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It took about a half hour for the action to begin. The first glimmers were nothing more than a faint sparkle, as if an unseen hand were tossing pinches of glitter behind our oars. As the sun faded, the darkness deepened and the shimmer intensified. Soon the sparkles gave way to radiant swirls and bizarre clouds that looked like glowing milk spilled into the black water. Thin streamers of light wrapped around the hulls of our kayaks as we pressed further into the darkness. I lifted my paddle out of the water. The glowing milk ran off it in sheets, each droplet hitting the water’s surface with an electric splash.

Given the seasonal and somewhat temperamental nature of the Russian River display, bioluminescent tides might seem a rare occurrence. But they are a global phenomenon, one that becomes increasingly common as you approach the equator. One of the most famous displays of bioluminescence is on Puerto Rico’s Puerto Mosquito, on Vieques Island, where the warm water glows an otherworldly blue. Here in the temperate waters of the Bay Area, where water temperatures are lower, the glow doesn’t reach the dazzling luminosity of the tropics. But one can sometimes experience bioluminescence in several places, including Tomales Bay, in Marin County, and Elkhorn Slough, in Monterey County.

The world of living light is strange, wonderful and staggeringly diverse. While only a handful of terrestrial species glow—fireflies, glowworms, fungi—it is an extremely common trait among organisms in the marine environment. According to Steven Haddock, a researcher at the Monterey Bay Aquarium Research Institute and a leading expert in bioluminescence, roughly 75 percent of marine organisms generate their own light. 

The variety of bioluminescent sea life is truly staggering, from the micron- to millimeter-scale dinoflagellates under our boats, to the glowing Dana octopus squid, which inhabits the deepest oceans and can grow to more than 7 feet long. “The ocean is kind of like the crucible for evolution,” said Haddock. “It has a much longer continuous history than any freshwater body. Also, the ocean is transparent, and most of it is dark, so it’s a great environment for bioluminescence to happen.”

The tiny single-celled organisms called dinoflagellates include the genus Alexandrium, seen here. They are bioluminescent and associated with red tides. Ken Koll, CC BY-NC 4.0

Two substances lay at the heart of these light-producing reactions, the compound luciferin and the enzyme luciferase. The luciferin found in dinoflagellates has molecular structure similar to that of chlorophyll, the photosynthetic compound in plants that allows them to convert sunlight to energy. (Scientists believe the luciferin in dinoflagellates may share an evolutionary lineage with chlorophyll) Like photosynthesis in reverse, bioluminescent animals expend cellular energy to generate light. (Other bioluminescent organisms that live deeper underwater use different chemical pathways and forms of luciferin to produce light.)

In the history of life on Earth, Haddock says, bioluminescence has evolved independently perhaps as many as 90 times in the history of life on earth. This suggests that the ability to emit light confers major advantages to sea creatures, particularly those living at great depths. One of the key advantages, says Haddock, is communication. “Light is a really effective way to send a signal over long distances and also to something that is much, much larger than yourself,” he said. Some species like flashlight fish and ostracods, tiny bioluminescent crustaceans, send morse code-like messages to attract mates; others, like the snaggle-toothed barbeled dragonfish mimic those signals to lure prey. “There really isn’t another mechanism like it—sound, chemicals, vibration. There’s just not another way to send a signal that rapidly.”

Counterillumination, or silhouette matching, is another use of bioluminescence that researchers are beginning to understand. “If you’re [an animal] swimming with this dim light coming down from the surface, you’re essentially casting a shadow or forming a silhouette,” Haddock said. Many predators lie in wait below, eyes pointed upward at the faintly illuminated surface, looking for the shadows of prey animals. To counter these ambushes, some animals, including certain species of squid, have evolved light emitting cells on their bellies to produce bioluminescent patterns that can almost perfectly match the color and brightness of the background. “It’s like a cloaking device, basically. It works by projecting whatever is behind in front of you.”

 But what use do very small organisms like the dinoflagellates in the waters of the Russian River have for bioluminescence? Researchers believe they use them primarily for defense, employing a biological “burglar alarm.” The incandescent light can startle prey animals or cause them to associate the bright colors with unpalatable, or even poisonous foods. (Many poisonous species sport bright colors to warn potential predators.) 

The sudden illumination also allows these tiny creatures to turn the tables on the animals that would make a meal of them. By switching on their natural light all at once, the dinoflagellates collectively create a biochemical floodlight that catches their assailants in the act, making them vulnerable to their own predators.

As the night progressed, Chandler became more difficult to keep up with, maneuvering his kayak in the darkness with swift, deft strokes. The only indication of his presence in the blackness was the blue glow of his light stick, which seemed to teleport around the bay at lightning speed.

We soon arrived in the darkest section of bay. The Milky Way arced overhead and cast a noticeable reflection on the water. With the sun completely gone, the bioluminescence became almost surreal, merging with the reflected stars from the sky. In its most striking manifestation, the dinoflagellates appeared as a kind of miniature aurora borealis rendered in the surface of the water. 

Chandler came to a halt in a deep section of bay. Here, he said, spawning salmon and steelhead returning to the Russian River later in the fall hold in this spot to acclimate to the freshwater upstream. “On dark nights you can see them swimming under the boat. Some are thirty inches long. You can see the glow around their bodies and their eyes light up like spotlights.”

And yet, bioluminescence is a delicate phenomenon, one that can be hard for our eyes—adapted as they are for seeing in the bright light of day—to detect. Even the modest shine from Jenner was, in places, enough to obscure the water’s glow. The biggest source of light pollution, however, was the river of traffic on Highway 1, which surged along the cliffside above us and frequently erased the shimmer from the surface of the bay.

There is also a dark twist to these beautiful natural light shows: bioluminescence can be a potent indicator of water pollution and climate change. Waterways like the Russian River, which pass through heavily urbanized or agricultural regions can deliver nitrogen and phosphorous from sewage effluent and fertilizer to their terminus at the ocean. This input of nutrients can kick microorganisms—including bioluminescent dinoflagellates—into reproductive overdrive, creating massive “blooms.” “What we found over the years is that often it’s blooming stronger in the estuary than in the open ocean,” said Suki Waters, founder and owner of WaterTreks. “It’s possible that they’re feeding off the nutrients from the agriculture.”

Blue glowing sand? Yes, that can happen, seen here at Bodega Head in Sonoma County. Damon Tighe, iNat CC BY-NC 4.0

Michael Latz, an emeritus researcher at the Scripps Institution of Oceanography at the University of California San Diego said that this can be the case, though location and climate often determines where and why bioluminescence occurs: “In places such as the bioluminescent bays of the Caribbean, where one bioluminescent species dominates and persists year-round, its bioluminescence can serve as a proxy of ecosystem health.” But in other regions, he noted, “high levels of bioluminescence are seasonal or episodic, and are associated with rainfall and nutrient runoff.”

As water temperatures rise, colonies of bioluminescent microorganisms can grow to massive sizes, in some cases covering hundreds of square miles. The strongest bioluminescence is often associated with so-called “red tides,” so named for their rusty red color in daytime. As the tiny creatures multiply, they turn the water a rusty red while rapidly depleting oxygen and creating large glowing deoxygenated dead zones.

Some bioluminescent species of dinoflagellates including Lingulodinium polyedra and Alexandrium monilatum secrete potent neurotoxins which can build up in aquatic ecosystems and poison marine wildlife. (The tribes of the Pacific Northwest have long recognized the glowing blooms as a warning not to harvest and consume shellfish, which can be contaminated with toxins secreted by dinoflagellates.) “You can have bioluminescence without the red tide,” Waters said. “But usually, if it’s a red tide, you’re also going to get a phenomenal bioluminescence because the ocean temperature is spiking.”

Red tides are relatively common along the southern California coast, where higher water temperatures are conducive to growth of microorganisms. Until recently they were an infrequent occurrence in the colder waters of northern California. But in 2022 and again in 2023, driven by rising ocean temperatures, massive red tides, parts of which glowed in the night, hit the Bay Area, causing a massive die-off of fishes, sharks, rays, crustaceans, mollusks, jellyfish and other species.

Like many natural phenomena thrown out of kilter in the new, carbon-loaded climate of the Anthropocene, bioluminescence can be a sign of ecological health or disruption.

After three hours of paddling in the darkness our arms were tired. My pants were also soaked through after having to get out of our kayak in the middle of the bay to drag it off a hidden sandbar. We followed our guide’s blue beacon back to shore. The group laughed giddily as we hauled our boats out of the water. The Russian River’s living light had, by nearly every measure, exceeded Chandler’s modest predictions. “I thought it was going to be good but not that good,” said one of the other paddlers, a woman in her mid-60s from Napa. “It was like rowing through a dream.”

As we drove home along the darkened coast, I told my son that the venture struck me as a kind of space travel on planet earth. Owen concurred, saying “There’s nothing like it, it’s almost alien. The closest thing isn’t on earth, it’s in the sky.”