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The main stem of the Eel River snakes northwesterly some 200 miles through canyons, forests and verdant farmland, gathering water from its many tributaries as it travels from its headwaters in the Mendocino National Forest to its terminus at the Pacific Ocean south of Humboldt Bay.

But this year, just 10 miles short of its final destination, the river vanishes from view as it passes by the small city of Fortuna, a sign that three years of drought is affecting traditionally water-rich Humboldt County, where the average annual rainfall of 55 inches is more than twice the state’s average.

Other factors, including sediment deposits in the river and escalating water diversions by marijuana cultivators have contributed to the rare, disappearing Eel River incident, according to state and federal fisheries authorities.

The river disappears but it does not actually cease running. It continues flowing under a deep gravel bed before reappearing 300 to 400 yards downstream, said Matt Goldsworthy, a fisheries biologist with the National Marine Fisheries Service.

“Some people are saying it stopped flowing,” he said. But “the water is still flowing below the gravel,” he said.

The differentiation means nothing to migratory fish, which, unless it rains soon, won’t be able to get past the barrier and head upriver to their spawning grounds this fall. That problem could turn out to be a blessing in disguise given the river conditions, Goldsworthy said, noting that the upstream spawning grounds may not be viable because of the drought.

The fall salmon run had not yet begun, so the barrier is preventing fish that are currently in the ocean from getting trapped in shallow, warm pools upstream, where they’d likely die, he said. Similarly, most of the out-migrating juvenile fish have already made it to the ocean.

“The timing is pretty good for fish,” Goldsworthy said.

If rain continues to shun the North Coast, there will be negative impacts to the fisheries, just not as dire as it would be had the timing been less fortuitous, he said.

It’s not uncommon for rivers and streams to disappear under ground for short stretches, but it’s a rare occurrence for the main branch of the Eel River and so close to the ocean, Goldsworthy said.

“Little reaches go dry. Usually it’s further upstream,” Goldsworthy said.

It last occurred at Fortuna, a city of 11,000, in the late 1980s, said state Fish and Wildlife spokesman Clark Blanchard. The bar at the mouth of the river also closed up that time, he said.

So far, cities and most farmers in the Eel River valley appear largely unaffected by the river’s decline. Despite near historic low flows in the Eel, only minimal, state-mandated water restrictions are in effect in towns, and agricultural fields are lush from irrigation operations that farmers in Mendocino, Sonoma and the Central valleys — where drought has made water a precious commodity — can only dream about this year.

Water users in Rio Dell, a small town upstream of the dry stretch of river, were briefly ordered to reduce water consumption to 50 gallons a day because of low river flows, but the state lifted the restriction after the city demonstrated there were no registered senior water rights holders being affected by its use.

Rio Dell’s city manager was not available Friday to discuss its water use. But its website states that the city does use surface flows from the Eel River. Fortuna, downstream along the dry stretch, does not. Its water is supplied by wells that currently are in good shape, said City Manager Regan Candelario.

John O’Hagan, assistant deputy director for water rights at the state water board, said the agency is looking into the river’s decline and water uses along it.

But “we haven’t had any calls from water rights holders” complaining their water is gone, something one would expect given the conditions, he said.

Elsewhere in the county, farmers and individuals dependent on wells and springs have reported shortages, said Humboldt and Trinity counties’ Agricultural Commissioner Jeff Dolf.

“This is an extraordinary drought” for the area, he said.

Goldsworthy said his agency had been monitoring the river’s decline over a couple of weeks and noted its subterranean move in the middle of last week. He said there likely are several factors involved in the river’s decline besides drought.

One is marijuana cultivation, which a state Fish and Wildlife study found is rampant in some watersheds in Humboldt and Mendocino counties. Pot production can and in some cases has used all the water available in some streams, the study reported.

Another factor is sediment. The Eel River has a huge sediment load and floods in 1955 and 1964 deposited large amounts of gravel downstream. Normally, heavy rains clear out some of the gravel deposits, but not in the past several years, Goldsworthy noted.

Forty years and more ago, the gravel problem would have been fixed by moving it with bulldozers but that’s no longer allowed, other than in exceptional cases, noted Doug Strehl, the mayor of Fortuna and a 58-year resident of the area.

While the Eel River has been hovering at historic lows, it would be even lower if not for recent releases from Lake Pillsbury, located in the Mendocino National Forest near the river’s headwaters. Officials have increased flows from the reservoir in response to the river’s decline, Goldsworthy said.

The situation isn’t good but Strehl said it’s not as bad as it looks and he’s not worried. Yet.

“If we don’t have any rain this winter . . . ,” he said.

You can reach Staff Writer Glenda Anderson at 462-6473 or glenda. anderson@pressdemocrat.com. On Twitter @MendoReporter

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