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Massive but controversial restoration project in the works for Upper Klamath Lake (Barnes and Agency Ranches)

by Alex Schwartz December 18, 2021

The U.S. Fish and Wildlife Service is evaluating a major restoration project on the shore of Upper Klamath Lake that could benefit species both above and below the water’s surface. If carried out, it would be the largest wetland restoration effort ever attempted for Upper Klamath Lake.

According to a draft environmental assessment released this summer, the USFWS hopes to breach levees that currently separate the Barnes and Agency Lake units of Upper Klamath National Wildlife Refuge from the western shore of Agency Lake, the northern arm of Upper Klamath Lake. Doing so would reconnect and restore more than 14,000 acres of historic fringe wetlands back to the lake.

Originally diked and drained by the Bureau of Reclamation beginning in the 1940s, the wetlands that became Barnes and Agency Lake ranches hosted grazing cattle during summer and pumped water to flood-irrigate pasture in winter. Fourmile and Sevenmile creeks, which originally flowed into the lake through the wetlands, were channelized and funneled into canals bordering the current property.

Reclamation purchased the plots in 1998 as water storage areas, allowing the creeks to flood them during the winter, then pumping that water into the lake in the spring to augment the Klamath Project’s water supply. However, pumping costs proved too expensive for Klamath Project irrigators and Reclamation abandoned the storage operation in 2013, transferring the land to Fish and Wildlife.

Since then, FWS has seasonally flooded the former ranches to produce emergent wetland habitat for bird species. According to the EA, more than 80,000 waterfowl have been counted molting on Upper Klamath Refuge in good years.

Klamath Basin Refuge Complex Manager Greg Austin said the proposed project, which has been in the works for more than a decade, would provide a host of benefits for the lake ecosystem.

“We spent a lot of time looking at what we wanted to get out of it,” Austin said. “The lake does need this. The lake historically was surrounded by wetlands, and we’re missing a big percentage of them now.”

In addition to being ideal bird habitat, the wetlands also filtered nutrients from creeks as they entered the lake (and from the lake itself as its water circulated through them), sequestering phosphorus into rich peat soils. They also provided habitat for numerous fish species, from redband trout to suckers, and smoothed the peaks and troughs of drought and flood by slowly absorbing and releasing water.

The loss of the majority of Upper Klamath Lake’s fringe wetlands has left it without these crucial sponges and filters, leading to toxic algae outbreaks that tank water quality and stress out endangered C’waam and Koptu, who later succumb to predation or fish disease.

While USFWS can’t manage the behavior of these wild species, Austin said they can work to restore their former habitats and provide the space and necessary functions for ecosystem recovery. The Barnes-Agency project hopes to accomplish just that.

“If you set the table, they’re going to show up,” he said.

Lessons learned

Mark Buettner, a fish biologist with the Klamath Tribes, said previous restoration efforts around Upper Klamath Lake helped inform the preliminary design of the Barnes-Agency project.

The Williamson River Delta restoration led by The Nature Conservancy, for example, removed dikes that had separated thousands of acres of wetland from the lake at the mouth of the Williamson River in the mid-2000s. However, because the farmland that had replaced the wetlands had subsided over many decades, much of the re-flooded area was too deep for aquatic plants to take root. Additionally, full removal of the dikes allowed winds and lake currents to influence the restored area, further inhibiting the re-establishment of wetland habitat.

Buettner said the preferred plan for Barnes-Agency outlined in the EA doesn’t plan to remove the dikes outright. Forming gaps in the barriers at key points will allow the free movement of water and fish while keeping those physical disturbances out. Once peat accumulates over many decades, then the dikes could be fully removed like they were on the Williamson River Delta.

“That was an unintended consequence of total removal of the levee versus what we’re looking at here, which is partial breaches,” Buettner said. “You don’t get this big expanse of water that would be exposed to wind and wave action.”

Additionally, USFWS plans to flood additional lands north of the Barnes-Agency units that were donated and put under easements with the refuge. These sit at a higher elevation than the units to the south, making them ideal emergent wetland habitat. Austin said a little less than half of the project will restore these seasonally dry habitats, while the areas closer to the lake will become open water where wocus and other submerged aquatic plants could grow.

The project also includes stream restoration on Fourmile and Sevenmile creeks, freeing them from their canals and directing them back into the sloughs, where the water will spread out through floating jungles that will absorb its nutrients before it reaches the lake. A potential 2,000-acre area on the project’s northeast flank, engineered in partnership with Trout Unlimited, would do the same thing to agricultural tailwater. Acting as a treatment wetland, it could accept drainage from ranches in the Wood River Valley, scrubbing out much of the runoff’s nutrients before releasing it back to the lake.

Buettner envisions this project to create an area similar to Pelican Bay, several miles to the south. Thanks to abundant wetlands and an infusion of high-quality water from several shoreline springs, Pelican Bay has become an area of refuge for endangered adult suckers fleeing water quality declines in the lake associated with cyanobacteria blooms. As the populations age without surviving young to replace them, biologists want to keep existing adult suckers alive for as long as possible.

“You could have a similar situation here where you’ve got these cold, clear-water creeks coming in, creating a Pelican Bay type of situation,” Buettner said.

The Klamath Tribes are working to limit excess nutrient loading on the tributaries to Upper Klamath Lake to improve water quality for C’waam and Koptu, but it’s a long game engaging a multitude of private landowners, federal agencies and restoration groups on miles of river. Buettner said this project could make a big dent in the lake’s phosphorus loading in a much shorter amount of time because it’s under federal management.

“In terms of trying to get back to a more historic form and function, that’s the important thing to do,” he said.

Irrigator concerns

But the Barnes-Agency project isn’t without its potential impacts. Through the National Environmental Policy Act process, several people representing Klamath Project irrigators and irrigation districts have written in opposition to the draft EA, pointing out that it didn’t adequately analyze how expanding the size Upper Klamath Lake by 14,000 acres could affect water management in the Klamath Basin.

USFWS did model how the project would change the lake’s total volume in water years 1981-2019, finding that, on average, usable water storage increased by up 17,183 acre-feet. Over that period, the analysis found no years in which the creation of more open water and wetland habitat, though leading to increased evapotranspiration, reduced the lake’s storage volume.

However, project irrigators have pointed out that even if storage increases, there could still be constraints on who that water is available to — or whether it becomes available at all.

“We recognize that the project would mean that there is more water in storage,” wrote Klamath Water Users Association Executive Director Paul Simmons in his comment letter. “This does not translate directly into improved water availability or reliability.”

Simmons said the concern is that a larger Upper Klamath Lake will take longer to fill and require more water to do so. The drop in lake levels resulting from the initial dike breaching aside, a separate analysis commissioned by Reclamation found that, in low water years since 1981, having a greater storage volume actually resulted in reductions to both the Klamath Project’s allocation and the amount of water released from Iron Gate Dam into the Klamath River.

That’s mainly because the three demands on Upper Klamath Lake — spawning habitat for suckers, river flows for salmon and irrigation diversions for the Klamath Project — all converge in the spring. Had Reclamation’s current Interim Operations Plan for 2021 been in effect throughout the past 40 years, the analysis they commissioned found that project allocations would have been generally lower in drier years and higher in wetter years due to the agency either hitting or missing Upper Klamath Lake’s spring target level.

According to the Bureau’s analysis, the project would receive an additional 35,000 acre-feet at maximum and lose about 21,000 acre-feet at minimum. However, to fill the lake in time to meet ESA requirements for suckers, river flows had to be reduced in all year types, with the greatest reductions to Iron Gate releases felt in the late winter and spring. That’s exactly when downriver biologists stress the need for flushing flows to dilute spores of the fish parasite C. shasta plaguing outmigrating salmon.

Gene Souza, manager of Klamath Irrigation District, wrote in his comment letter that he expected the National Marine Fisheries Service, which authors the Biological Opinion for threatened Klamath River Coho salmon, would find those flow reductions “unacceptable” and require further cuts to project diversions.

“It is more likely, during consultation efforts, the burden of this action will be squarely placed upon the shoulders of Klamath Project irrigators,” Souza wrote.

Souza and Simmons both made it clear that they don’t have any issues with the Barnes-Agency project’s concept, not disputing that it could bring real benefits to birds and endangered suckers. But they said they couldn’t support implementing a project that might significantly reduce water availability to irrigators in some years without adjusting the way water is allocated in the basin.

“If we’re going to start doing projects that take away water from one interest, that needs to occur as part of a more comprehensive package where there’s clear quid-pro-quos,” Simmons said. “It’s like, ‘Oh, we’re out to torpedo it.’ Well, that’s not our goal, but we don’t want to get hurt. Let’s try to solve problems, not create new ones — or bigger ones.”

While he acknowledged its potential downstream impacts due to the basin’s water management setup, Austin said modeling how the Barnes-Agency project would influence Reclamation’s operations wasn’t within the EA’s scope because the refuge doesn’t have control over how the Bureau will allocate water. It’s difficult to predict how the expansion of Upper Klamath Lake would impact management decisions because those management decisions are frequently in flux.

“You don’t have a crystal ball of what might go into the next iteration (of the Biological Opinion),” Austin said.

Still, Austin said USFWS plans to closely review the Reclamation analysis and have a dialogue with water users and downstream stakeholders about the impacts it discusses. He said the goal of NEPA’s public comment component is to alert federal agencies to gaps in their evaluations.

“That’s exactly what you hope for,” Austin said. “Usually, we write NEPA and we’ll get two or three comments. This is one that a lot of people are interested in.”

Reclamation and both Services are currently in ESA consultation to develop the Bureau’s next operations plan, and Buettner said that plan could potentially accommodate the potential for a bigger Upper Klamath Lake, similarly to how the BiOps incorporate the impending removal of four dams on the Klamath River.

Austin said the project still has not undergone an engineering design, let alone moved past the NEPA process, so conversations about its potential impacts will likely continue as agencies analyze the data on hand. He said USFWS acknowledges the need not to rush a project of this scale, regardless of the benefits.

“We want to make sure we’re doing the right thing,” Austin said. “It’s going to take a little more time — a lot of eyes are on it.”




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