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Wasting water to kill fish?
Record Chinook salmon in Stanislaus River
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The Stanislaus River Salmon Festival is Saturday.

And so far a record 6,000 endangered Chinook salmon have passed through a high-tech weir near Riverbank.

The festival at Stanislaus River Park at Knights Ferry from 10 a.m. to 3 p.m. gives you a chance to see spawning salmon from the historic wooden bridge or via a monitor that’ll be setup using underwater cameras. But even with music, hands-on activities for kids, fly fishing demonstrations, and other festival trappings it’ll be tough to get scientists that make a living monitoring the river in a jovial mood.

“There’s no cause for celebration,” noted biologist and Fishbo principal Andrea Fuller who has been studying the Stanislaus River and its fish for 20 years.

That’s because Fuller said the federal government’s pulse flow releases from New Melones Reservoir during the fourth year of severe drought has created conditions that have water temperatures 5 degrees higher than normal. That is expected to translate into a much higher kill rate for eggs.

The pulse flows were a major point of contention between the South San Joaquin Irrigation District/Oakdale Irrigation District and state/federal agencies. At one point, SSJID expressed concern the decision by the state and federal agencies to follow policy instead of making drought decisions based on hard data would eventually mean the New Melones releases would be simply luring Chinook salmon to their death.

Events now unfolding in the Stanislaus River are supporting that position.

The expected high kill also comes on the heels of data collected by Fishbo that showed a large chunk of this year’s record Chinook salmon arrived ahead of the latest 23,000 acre feet of water released for the purpose of attracting the fish. That was enough water to roughly meet the needs of Manteca and Tracy for a year.

The salmon count by Fishbo — hired jointly by the SSJID and OID to monitor the river and restore habitat during the past 10 years — is significantly more accurate than the state’s methods.

Fishbo uses a narrow weir near Riverbank employing infrared technology to get photos of silhouettes of all fish passing through. That compares to the state’s method that tags fish and then returns and collects dead carcasses whether they are tagged or not to statistically determine survival rates and population count.

The stakes of getting the fish data right and making water release decisions based on that is extremely high. The water being used could have gone toward agricultural and urban use or even maintaining year round river flows. As such fish releases driven by policy and not data threatens water supplies for SSJID, OID, as well as the cities of Manteca, Lathrop, and Tracy.

Water policy has allowed

bass population to grow

at detriment of salmon

Fuller noted, as an example, decisions by the state to hold fast to policy and not make decisions based on hard data that is collected set the stage for a steady decline of threatened fish species in the Delta since 2003. Declining native fish populations predate the current drought.

The policies have essentially created steady water conditions in the Delta throughout most of the year. Many native fish are stressed mainly because bass — a non-native fish — thrives in such steady water conditions. That in turn creates even more predators to kill off the Chinook salmon and other fish.

The survival rate for Chinook salmon is between 2 and 5 percent by the time they reach the western end of the Delta and enter San Francisco Bay.

Fuller also noted the vast majority of Chinook counted on the Stanislaus River are those marked as hatchery fish.

Water being released at New Melones is currently 62 degrees when it reaches Goodwin Dam above Knights Ferry. That’s because the water being released is from the shallow pool of 265,710 acre feet of water remaining in the reservoir that has a capacity of 2.4 million acre feet. Shallow water is warmer.

The temperature at Knights Ferry is now 60 degrees, 5 degrees above average.

Fuller said the cooler weather has helped somewhat but the shallow reservoir is creating lethal conditions for the Chinook salmon.

Issue with Chinook

Salmon also on

Sacramento River

“We’re on track to get one of the highest abundances of returning adult salmon in the last 12 years,” Fuller said. “But the sad thing is we don’t expect much of anything from them in terms of reproduction. There isn’t a single riffle in that river with suitable temperature conditions for their eggs.” 

With the cold water gone thanks to pulse flows, managers are out of options to help this year’s salmon. Fuller noted that similar challenges have been encountered at Lake Shasta in trying to maintain temperatures cool enough for winter-run Chinook salmon on the Sacramento River.

 One explanation for the banner number of adult Chinook salmon on the Stanislaus River this year is the poor conditions on the San Joaquin, Tuolumne and Merced rivers. The San Joaquin River upstream of the Stanislaus River confluence, as well as the Tuolumne and Merced rivers, is severely clogged with invasive water hyacinth, likely creating a barrier that causes many fish to seek out the Stanislaus River instead. Fishbo’s fish-counting weir on the Tuolumne River has only observed 78 salmon as of Nov. 8, and the California Department of Fish and Wildlife has reported only about 22 salmon in the Merced River this year.


While students are taught the basic salmon lifecycle of traveling from river to ocean to river, the scenario in the Stanislaus River is not quite so simple. Fishbo’s scientists believe that almost all of these returning fish were not actually born on the Stanislaus River, but instead came from hatcheries, either on the Merced River or in the Sacramento River basin. While a record salmon migration would seem like a success, digging deeper actually reveals a number of the challenges facing salmon in the Central Valley.

 Funding for salmon monitoring on the Stanislaus River, including the fish-counting weir, is provided by the Oakdale Irrigation District, the South San Joaquin Irrigation District and the Tri-Dam Authority, with equipment on loan from the U.S. Fish and Wildlife Service. FISHBIO has been sharing weekly updates of the weir fish counts with third- and fourth-grade teachers in Oakdale, Ripon and Modesto as part of the company’s Three Rivers Education Program. Students have been able to graph the salmon migration as it happens and compare this real fisheries data to the migration patterns of previous years.