October | 2024 | California Fisheries Blog

The final steps in Klamath River dam removal are complete, and the first salmon has migrated upstream into the dam-removal reach in over 100 years. The four reservoirs were drained last winter and the dams removed this summer. The river is now free in its natural channel. Two dams remain up at Klamath Lake (Keno and Link dams – not part of the project), but the lower four hydroelectric project dams – three in Oregon and one in California – are gone. With the demolition of the last of these lower four dams this summer, the Klamath is running free from its headwaters in southeastern Oregon to its mouth in the Pacific Ocean on Yurok tribal lands in northwestern California. Hundreds of miles of spawning grounds are open to Chinook salmon, Coho salmon, and steelhead for the first time in more than a century.

The dam-removal process was not without problems, although these problems were generally foreseen in planning and permitting. First was the reservoir draining process this past winter, when the reservoirs were drained, from mid-January to mid-February. In the four-dam reach and in the Klamath River downstream, high suspended fine sediment and low dissolved oxygen were problems, though determined of limited risk to the few salmon and steelhead in the river at that time. However, the Assisted Sediment Evacuation project element (Figure 1) continued past its prescribed end date of March 15 into early April, extending the presence of lethal levels of suspended sediment into the early juvenile salmon and steelhead emigration season from tributaries, a season that includes March. Lethal levels of suspended sediment extended downstream over 100 miles as far as Orleans (Figures 2 and 3).

Subsequently, during the summer, dam infrastructure was removed to provide full salmon passage past the dam sites. Low flows necessary to access the dam sites for material removal, and high summer air temperatures, resulted in very warm water temperatures beginning in July. Removal of coffer dams and further Assistant Sediment Evacuation at the dam sites (Figure 4) led to the return of lethal sediment levels in the river below Iron Gate (see Figure 2). On three days, dissolved oxygen below Iron Gate reached zero.

Though approved by the project technical team, the high suspended sediment level through September likely hindered a major portion of the fall-run Chinook salmon run up the Klamath River (Figure 5). Only 60 adult salmon were reported at the Shasta River trap as of early October, by which time daily numbers are usually in the hundreds. Numbers at other traps at other tributaries were even lower, which perhaps explains why only one salmon has been seen at the new sonar station above the Iron Gate Dam site.

With the cessation of Assisted Sediment Evacuation at the end of September, the hope is that suspended sediment levels will return to the low pre-summer levels and fall-run Chinook salmon will recommence their migration upriver. The river should be clear for late fall and winter runs of coho salmon and steelhead.

The use of Assisted Sediment Evacuation in winter and early spring, and then again in late summer, will remain controversial, if only in that it was applied under an extended time frame from the original planning and permitting documents. The summer application was certainly a surprise to local stakeholders,¹ who were shocked by the extent and duration of the muddy and smelly river conditions. A condition of zero dissolved oxygen for 50 miles below Iron Gate dam for two days in September was not approved under the permits issued by the state or federal governments.

In my opinion, the initial and final evacuation of muddy sediment should not have been implemented by using excavators to dump sediment directly into the river. A better option would have been natural removal by winter storm events that would have provided a much higher dilution factor and would have had a better chance for a non-lethal concentration of suspended sediment. Furthermore, more of the sediment should have been removed or stored in upper terraces and not allowed to enter the river.

The NOAA Fisheries final assessment of the dam removal effort failed to acknowledge the problems and potential consequences of the spring or summer events.

“Heavy equipment removed the final obstacle separating the Klamath River from the Pacific Ocean on Tuesday. The reconnected river was turbid but remained safe for fish after crews took steps to avoid erosion and impacts to water quality.” The river was not safe for salmon or steelhead for over 100 miles downstream.

“Crews used a strategy of releasing sediment and organic material that muddied the river but avoided a decline in dissolved oxygen that could have otherwise harmed fish.” Untrue. Both dissolved oxygen and suspended sediment levels were lethal. Hopefully, many fish were able to avoid these conditions.

Figure 1. Photo of Assisted Sediment Evacuation process from Iron Gate Reservoir in March 2024. (KRRC video screengrab)

Figure 2. Turbidity (as measured in FNUs) in lower Klamath River in 2024. (Karuk water quality data). See Figure 3 for locations. Red line is approximate lethal concentration for salmon.

Figure 3. Lower Klamath River USGS water quality sampling stations. (source: USGS)

Figure 4. Assisted Sediment Evacuation associated with the removal of Copco No. 1 Dam cofferdam on August 14, 2024. The mainstem Klamath flow is coming from bypass tunnel in upper center of photo.

Figure 5. Timing of fall-run salmon return (daily counts) to the lower Shasta River weir-trap in years 2017-2020. (CDFW data)

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A weekly survey by the US Fish and Wildlife Service¹ targeting Delta smelt captured one Delta smelt in early August 2024 (Figure 1). It was the first and only Delta smelt caught this summer in that smelt-targeted survey in the Bay-Delta Estuary. A late April IEP juvenile fish survey (the 20-mm Survey) caught several juvenile Delta smelt in the same area (Figure 2).

What is unique about this location in Suisun Bay? In 2024 the low-salinity-zone (LSZ) has been located in Suisun Bay for most of the spring and summer, as Delta outflows have been maintained at 8,000-12,000 cfs (Figure 3). The LSZ is the critical spring-summer habitat of the Delta smelt (a salinity range related to high survival in the population). When the LSZ is in Suisun Bay, it generally remains within the maximum temperature tolerance of Delta smelt (70-72^oF). When Delta outflow falls below about 7,000-8,000 cfs, the LSZ moves east into the warmer Delta. Delta water quality standards (D-1641) require a minimum outflow of 7,000 cfs in wetter years for this reason. When it is east in the Delta, the LSZ tends to have warmer water due to higher air temperatures. The Delta smelt biological opinions have a provision called “Fall X2” that requires extra Delta outflow in late summer to help ensure Delta smelt are west in Suisun Bay (Figure 4), where they have higher survival potential.

The LSZ does not occupy a large area – it is generally a small mixing zone where fresher water meets the saltier water. The LSZ moves up and down the estuary with the monthly and daily tidal cycles. The one smelt was caught in early August, when the LSZ happened to be at that net sampling location (Figure 5) because of the relatively high Delta outflows in summer of above-normal water year 2024. In contrast, much lower Delta outflows in summer of drought year 2022 brought saltier water to Suisun Bay (Figure 6), and the LSZ was upstream in the warmer lower Sacramento River channel of the Delta near Rio Vista (Figure 7).

In closing, there are a few Delta smelt left – but it is near the end of over five decades of population decline that has brought them single digits away from extinction (Figure 8). The cause in large part has been the devasting effects of low spring-summer Delta outflows in drier years that maintained the LSZ upstream of the Bay in the warmer Delta, where the smelt cannot survive. Efforts to protect the smelt in only in wetter years by requiring higher Delta outflows were positive, but requirements in wetter years alone are not enough: the smelt only live one year. The only option left is to maintain the 10,000-12,000 cfs Delta outflow in all years, raise the captured brood stock at UC Davis for release in the LSZ in the Bay, and hope the species can recover. The cost would be about 1 million acre-feet of water supply in the drier years over the summer.

The choice was made for us by DWR and in the soon-to-be-released US Fish and Wildlife Service updated biological opinion on the long-term effects of the state and federal water projects. The most recent opinion issued in 2019 stated the projects do not jeopardize the viability of the Delta smelt population. Now we seem intent on removing the one remaining lonely smelt. Just remember, the Delta smelt were supposed to be the “canary in the coal mine.”