Scott River at Blacks Bridge

The Scott River at Blacks Bridge, north of Etna. Due to irrigators diverting surface water and pumping groundwater during an extreme drought in the watershed, the river’s main stem ran dry last week, trapping threatened Coho salmon in small pools.

Relief may be soon be arriving to salmon imperiled by exceptionally low flows in the Scott and Shasta rivers this summer.

The California State Water Resources Control Board adopted regulations Tuesday to limit irrigation diversions and groundwater pumping in both watersheds, which produce a significant proportion of the Klamath Basin’s salmon populations.

The Scott River contains an evolutionary significant unit of Southern Oregon Northern California Coast Coho Salmon, which are listed as threatened under the Endangered Species Act. The sub-basins also produce as much as 20% of the Klamath’s fall Chinook runs. Both species are culturally important food sources to the Karuk, Yurok, Hoopa Valley and Quartz Valley tribes and provide an economic resource for ocean fishermen on the Northern California coast.

In addition to concern over the viability of the fish, the Tribe’s reservation sits within the Scott Valley and relies on water levels for gathering and even drinking water. Wells have gone dry in previous years due to the river’s dewatering.

“The water usage in the Scott River Basin favors one community at the expense of the tribal community,” said Quartz Valley Indian Reservation Chairman Harold Bennett. “The existing laws are designed to prevent these environmental conditions, but without enforcement we are forced to live with the outcome of voluntary efforts which are not meeting the needs of the Tribe.”

Through authority granted by Governor Gavin Newsom’s drought declaration in Siskiyou County, the Water Board will issue the curtailments on an emergency basis to provide minimum flows for the fish in early fall and through late next summer.

The goal is to allow adult coho and fall Chinook to access spawning habitat in the rivers’ tributaries, many of which have become disconnected from the mainstem due to extremely low water levels. If spawning habitat remains limited in the Scott, the coho may spawn on top of the Chinook eggs, suffocating them. Last year, the Scott was so dewatered in November and December that coho were blocked for a period from accessing its tributaries to spawn.

Additionally, some coho juveniles, which rear in the Scott Watershed for a year after they hatch before migrating to the ocean the following spring, have been trapped in pools in the Scott’s dewatered stretches this summer, making them vulnerable to predation and poor water quality conditions.

The California Department of Fish and Wildlife penned several letters to the Water Board this summer urging regulators to adopt emergency flow requirements for the Scott and Shasta, citing this year’s exceptional drought conditions. It was a rare move for the agency, and the first time they’ve recommended emergency flows in the Klamath Basin.

But biologists assert that drought isn’t the only limiting factor to salmon habitat in the two rivers. Because environmental base flows hold junior water rights (if at all), irrigators in the Scott and Shasta Valleys don’t have to limit diversions or groundwater pumping to leave water for the fish, instead diverting to the full extent of their water rights even in years when such diversions dewater the streams.

“There’s been an argument made that because of the low flows, we can’t achieve the recommendation. But we really need to acknowledge that that’s an impaired low flow,” said Joe Croteau, Klamath program manager for CDFW.

Agricultural impacts

According to U.S. Geological Survey streamflow data, the Scott’s average September flow was 33.1 cubic feet per second from the beginning of its period of record through 1980. After the river and several of its tributaries underwent a water rights adjudication that year and users began drilling irrigation wells, diversions from the river began increasing in late summer, along with the frequency of drought years. Since 1980, the average September flow in the Scott River has been 9.7 CFS, and a 2008 study attributed 61% of that decline to factors other than climate change.

In the Shasta, upstream gages tend to read higher flows than downstream ones during the height of the irrigation season. And because the system is largely spring-fed from glaciers on Mt. Shasta and tends to be more naturally resilient in drought years, hydrographs show flows jumping significantly in the early fall once diversions drop off.

Groundwater pumping is more present in the Scott than the Shasta, and hydrological studies of the watershed show that groundwater levels are closely related to surface flows. However, unlike the Shasta, flows in the Scott may take longer to respond to reduced groundwater pumping as the water table slowly rises. But scientists and regulators decided to take their chances and hope the effects (ideally correlated with some fall rain) show up in time for the Fall Chinooks’ arrival.

“There’s definitely a high demand for water,” Croteau said. “We can’t, as the only trustee agency, not do anything. Every CFS matters to us.”

Supporters of the emergency regulations point out that while other agricultural areas throughout the West have had to reduce water usage and struggle to produce crops due to the region’s historic drought, fields in the Scott and Shasta Valleys are lush with crops while some stretches of the river have been reduced to pools.

“The worst water conditions in history led federal agencies to shut off 1,300 farms in the Upper Basin, but in the Scott Valley water users continue business as usual,” Karuk Tribal Chairman Russell ‘Buster’ Attebery said in a news release last month. “They are dewatering the last stronghold of Coho salmon in the Klamath basin driving them to extinction.”

A cursory economic analysis completed by Water Board staff concerning the regulations’ impact estimated that Scott Valley irrigators’ fourth cuttings of alfalfa (translating to a yield reduced by 11%) would be affected. Klamath Project growers may be lucky to get two or three this year.

If approved by the California Office of Administrative Law, the regulations will be in effect in 10 days and the Water Board will be able to issue curtailments in order of water right priority date to diverters in both sub-basins. The regulations require a Scott River flow of 33 CFS in September, 40 in October and 60 in November at Fort Jones gage. The Shasta River at Yreka gage must be kept at 50 CFS in September, 125 in October and 150 in November.

Andy Marx, president of Friends of the Shasta River, said the regulations are a long time coming.

“We’re heartened to see that the state is doing what it takes to bring the salmon home,” he said.

Voluntary measures not enough

However, if water rights holders can prove that they’ve already reduced the amount of water they’ve diverted since last year by the same amount as their curtailment through a variety of measures, like localized fish passage, cold water refugia development or redd protection, language in the emergency regulations allows them to work with the Water Board to potentially reduce their curtailments. The Water Board adopted the provision in part through consultation with local agricultural stakeholders.

“We’re not entirely excited about the end product, but we always felt like we were heard,” said Ryan Walker, president of the Siskiyou County Farm Bureau. “We want to find ways to get through this year and next year and not have for sale signs on ranches.”

Indoor domestic use, energy sources, fire prevention, public health efforts and reforestation operations will be exempt from the regulations, along with non-consumptive water use and minimum diversions for livestock watering.

Efforts have been made in recent years to work with landowners to engage in voluntary watershed improvements, but not at the scale Tribes and some watershed advocates say is needed to recover salmon populations. Many believe water users need a stick in addition to a carrot to improve fish habitat.

“We’ve seen what 20 years of voluntary actions have done, and it’s not enough. While they’re great and we are thankful for anybody that’s done anything voluntarily, it’s not enough,” said Crystal Robinson, environmental director for the Quartz Valley Indian Reservation and an advisor to the Tribe on environmental matters. “I am hopeful but skeptical that voluntary efforts will result in the desired flow outcomes.”

Walker said the regulations may confirm Siskiyou County water users’ fears that the state was encouraging efficiency and restoration projects only to bring down the regulatory hammer anyway. He expressed concern that it could jeopardize voluntary efforts in the long run.

“Those guys are coming by and talking to me now and saying, ‘See, we told you. When we cut our water then, they weren’t going to give us credit, and they were just going to ask for us to cut some more,’” Walker said.

Water Board Chairman Joaquin Esquivel said the emergency regulations are part of a longer-term effort by CDFW and the Water Board to provide reliable environmental flows in the Scott and Shasta Rivers. As more science becomes available and regulators evaluate the effectiveness of curtailments on salmon habitat over the next year, stakeholders will be in a better position to understand how landowners must adapt to help fish.

“This doesn’t conclude our work here at all, and actually just starts it,” he said.