Category Archives: Northern California

WaterFix NMFS Biological Opinion Conclusions on Salmon in the Delta

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The National Marine Fisheries Service’s biological opinion (NMFS BO) on the proposed “California WaterFix” (Delta Twin-Tunnels Project) concludes there will be no significant effect on protected salmon, steelhead, and sturgeon in the Central Valley. In this post, I address the conclusions in the NMFS BO on the potential effects of WaterFix on salmon and steelhead in the Delta. This is one in a series of posts on the WaterFix. Within that series, it is the second post of the series on the NMFS BO.

The NMFS BO concludes that WaterFix operations would have significant adverse effects on salmon, steelhead, and sturgeon and their critical habitat in the Central Valley from changes brought about by the WaterFix Twin Tunnels Project. In contrast, the NMFS BO also states that the WaterFix is not likely to jeopardize the species or adversely modify their critical habitat. How such contradictory conclusions are possible, especially for the rather demonstrable Delta effects, is simply beyond reason. Previous drafts of the BO had not made that jump. There is no amount of adaptive management within reason, especially given past poor performance in operating the water projects and managing effects on fish, that can alleviate the potential great risks to Central Valley fishes from the adding the WaterFix Twin Tunnels to the state and federal water projects.

The “new” NMFS BO focuses on changes in flow patterns in the Delta below the three proposed diversion points in the North Delta. The diversions of up to 9,000 cubic feet per second (cfs) would change flow and flow splits downstream in Steamboat, Sutter, and Georgianna sloughs and the Delta Cross Channel, as well as in the main Sacramento River channel. As a consequence, freshwater flows entering the interior Delta from the north Delta would also change, as would Delta outflow to the Bay to the west. Young salmon, steelhead, and sturgeon from the Sacramento River and San Joaquin River basins would be affected by these changes upon entering the Delta on their way to the Bay and ocean.

The NMFS BO concludes that the up-to-9000 cfs diversion of the WaterFix would reduce channel velocities below the intakes in the north Delta. “Under the PA [Proposed Alternative] water velocities in the north Delta would be lower…. This would increase migratory travel time and potentially increase the risk of predation for juvenile salmonids.” (p. 602) In the past, based on my own assessments, survival of hatchery and wild salmon and steelhead to the Bay may have been reduced by 50-to-90 percent based on differential survival of marked hatchery smolts released above and below the Delta under differing flow regimes. The NMFS effects assessment is based on survival of radio tagged, large, late-fall hatchery smolts during the winter; this indicates just a small differential in survival. The real effect is likely somewhere in between and highly variable depending on a wide range of circumstances. No doubt a serious concern remains for the future of the various listed species and success potential of future commercial and recreational fisheries.

The greatest risks are to pre-smolt winter-run salmon in the fall season and to juvenile spring-run and fall-run salmon and steelhead in the spring.

“In the South Delta, median velocities generally increase under the PA…. The positive change in velocity would decrease migratory travel time and reduce predation risk for juvenile salmonids.” (p. 602) The conclusion is that exports from the south Delta will decline from November through June because of WaterFix. That simply is not true, because south Delta exports are already constrained during those months. WaterFix would not change those overall constraints; it would only add to the overall diversion capacity. Export restrictions based on net flows will remain the same; thus there will be no changes in rules governing the south Delta exports. Furthermore, the 9,000 cfs taken by WaterFix will reduce Sacramento River freshwater inflow into the central and south Delta, increasing any effects of south Delta diversions on the interior Delta’s hydrodynamics. The relative effects on San Joaquin River Delta inflows will remain the same or even increase.

“In the Central Delta, there is little difference in magnitude of channel velocities between the NAA [No Action Alternative] and PA.” (p. 602) While it is true there is little difference for channel velocities in this highly tidally driven region, it is not true for freshwater inflow, salinity gradients, and water temperatures, or for relative flow signature differences for the San Joaquin and Sacramento Rivers within the central Delta. The loss of Sacramento River freshwater inflow into the central Delta via Georgianna Slough and the Delta Cross Channel (when open) is significant. Tidal inflows from the west Delta into the central and south Delta in the San Joaquin and False River channels will increase, potentially reducing survival of San Joaquin salmon and steelhead. Sacramento River salmon and steelhead survival, already reduced by lower flows below the tunnel intakes, would be further reduced by lower survival of fish that passed through Georgianna Slough or the Delta Cross Channel, or through cross-Delta movement through Three-Mile Slough.

“In the North Delta, reverse flows would increase in most water years and months…. In the North Delta, the PA had a higher proportion of each day with negative velocities (reverse flow) particularly in Steamboat Slough and Sacramento River downstream of Georgiana Slough”. (p. 602) The loss of freshwater inflow to the WaterFix Twin-Tunnel diversion would decrease the extent in location and timing of unidirectional flow in the tidal Sacramento River (Figure 1). Diversions during times when Freeport flows were in the range of 15,000-35,000 cfs would change the river from virtually non-tidal to tidal.

Figure 1. Example period: flows at Freeport March-July 2017. Red arrow denotes 9,000 cfs WaterFix tunnel diversions above the 35,000 cfs inflow. WaterFix diversions would be minimal below 15,000 cfs inflow. Green line denotes point at which flow would become tidally influenced with WaterFix as seen after June 15 when hourly flows varied from 5000 to 15,000 cfs during a tidal cycle. Note: for location of gages, see Figure 4 map.

The effect downstream at the flow splits of the Sacramento River at Georgianna Slough and Steamboat Slough is even more pronounced (Figures 2 and 3). In the Sacramento River below the Georgianna Slough split, flood tides would turn negative earlier in the season with upstream WaterFix diversions (Figure 2). Likewise, Steamboat Slough flood tides would turn negative with WaterFix when Freeport flows fall to 25,000 cfs. In 2017, that would have meant negative flows nearly a month earlier with WaterFix (Figure 3). Not only do WaterFix diversions reduce flows in the northern Delta channels, they would turn migration period conditions poorer (reverse flows and higher water temperatures) nearly a month earlier than under present conditions. “In order to more thoroughly evaluate the impact of reverse flows on migrating salmon, NMFS undertook an additional analysis. The likelihood of juvenile fish entering migratory routes with reduced survival increases with the daily probability of flow reversal, or with increases in the proportion of each day with flow reversals. The probability of juvenile Chinook salmon getting entrained into migratory routes of lower survival like Georgiana Slough and the Delta Cross Channel is highest during reverse-flow flood tides (Perry et al. 2015). In addition, the proportion of fish entrained into Georgiana Slough on a daily basis increases with the proportion of a day that the Sacramento River downstream of Georgiana Slough flows in reverse (Perry et al. 2010). Consequently, diverting water from the Sacramento River could increase the frequency and duration of reverse-flow conditions, thereby increasing travel time as well as the proportion of fish entrained into the interior Delta where survival probabilities are lower than in the Sacramento River (Perry et al., 2010 and 2015)…. In the north Delta, increase in flow reversals downstream of Georgiana Slough are of concern for migrating salmonids…. Increases in flow reversals would likely reduce the survival probability of outmigrating smolts by moving them back upstream, increasing their exposure to junctions that lead to migratory routes of lower survival, such as in Georgiana Slough.” (p. 603)

Figure 2. Example period: flows at Georgianna Slough flow split March-July 2017. Red line notes when condition in Sacramento River below Georgianna Sough at which flood tides reverse river flow – when Freeport flow is below 25,000 cfs. In contrast, flows in Georgianna Slough would not become negative.

Figure 3. Example period: flow in Steamboat Slough below split March-July 2017. Flow in Steamboat Slough becomes negative when Freeport Sacramento River flow falls below 25,000 cfs. Under WaterFix, Steamboat Slough flows could become negative at Freeport flows below 34,000 cfs.

“The proposed NDD bypass rules include a commitment to an operational constraint that the amount of flow withdrawn at the NDD cannot exacerbate reverse flows (i.e., increase the frequency, magnitude, or duration of negative velocities) at the Georgiana Slough junction from December through June beyond what would occur in NAA. However, the BA does not describe the methods or the modeling that would show how this would be achieved. Specifically, the BA does not describe: 1. The extent that the proposed NDD bypass rules may affect the frequency, magnitude and duration of reverse flows in the lower Sacramento River; 2. The description of how real-time monitoring could be implemented to meet the criteria of not increasing reverse flows; 3. The modeling simulations that would show how this criteria is being met and therefore provide reasonably accurate bypass flow levels.” (p. 603).

In the example shown in Figures 2 and 3 above, WaterFix diversions would exacerbate reverse flows unless no diversion was allowed below a 35,000 cfs Freeport flow, a commitment not made in WaterFix proposal.

This is a major flaw in the NMFS BO assessment. Even NMFS acknowledges this fact: “The probability of a flow reversal in the Sacramento River downstream of Georgiana Slough occurring at some time during a 24-hour period is one hundred percent when Sacramento River flows at Freeport are less than 13,000 cfs (Figure 2-118 top panel). Likewise, when flows are greater than 23,000 cfs, flow reversals are not expected to occur at the Georgiana Slough junction.” (p. 606) A flow of 23,000 cfs would occur below the tunnel diversions when Freeport flow is 32,000 cfs.

“The following assumptions were used: 1) the NDD bypass rules are applied based on mean daily Sacramento River discharge at Freeport, and 2) water is diverted at a constant rate over an entire day such that the bypass flow is constant over the day. The analysis adheres to a strict interpretation of the NDD bypass rules and does not include flow variations at sub-daily timescales.” (p. 606) Note that diverting 9000 cfs on a flood tide with Freeport flow at 30,000 cfs would cause a flow reversal in Steamboat Slough and in the Sacramento River below the split at Georgiana Slough (Figures 2 and 3).

“October-November operations can greatly increase the probability of reverse flow; for example, when flows at Freeport are between 20,000 to 25,000 cfs there would be ~100% increase in flow reversals under the PA (Figure 2-124)… .(p. 606) The months with the largest increases in travel time for both the PA and L1 occur during the off-peak Chinook salmon migratory months of October, November, and June. During the peak Chinook salmon migratory window of December through April, February and March have the largest increases in travel time under the PA.” (p. 615) Such flows may occur in October-November from early storms, and a large influx of winter-run salmon pre-smolts would be expected to enter the north Delta under these circumstances. NMFS expects that restrictions on diversions during early pulses and changes to Delta Cross Channel operations would protect winter-run.

“However, if flow in November becomes sufficient through storm runoff events to trigger winter-run emigration towards the Delta, a pulse protection will apply that will limit diversions to low level pumping for a certain amount of days or until fish presence is not detected based on real-time management criteria. Without this protection, early emigrating winter-run would be subject to some of the more extreme diversion levels allowed, probability of reverse flows would increase, and winter-run Chinook salmon would face greater risk of entrainment into interior Delta and overall lowered survival.” (p. 625) WaterFix does not propose to protect all fall pulses, nor winter flow pulses. There would be no restrictions on south Delta diversions, which would be 11,400 cfs under these conditions. The WaterFix would thus exacerbate the existing level of impacts, which are quite serious in the fall of wetter years.

NMFS also notes potential serious consequence to spring-run and fall-run salmon: “May has a unique set of NDD bypass rules that is slightly less protective than the diversion rules in December through April because Level 2 or 3 could be enacted if bypass flow criteria have been met. 5% to 13% of spring run Chinook salmon smolts are expected to be in the Delta during this month (Table 2-171). They may experience slightly longer travel times than smolts traveling during earlier months given the same inflow at Freeport. This would be due to lower velocities that may result from less restrictive diversions as defined by the NDD bypass rules.” (p. 631) Most Sacramento Valley hatchery fall-run smolts are released into rivers or the Delta in late April and early May – they too are vulnerable to WaterFix-induced reverse flows in the Delta.

  • NMFS eventually concludes that reductions in survival in the north Delta are balanced by increased survival in the south Delta: “Interpretation of these analyses must also consider that small changes in absolute survival could translate to a large effect to a population, especially in years when overall Delta survival is low. The 2-7% increase in Delta survival that would occur if entrainment into the interior Delta were eliminated (Perry et al. 2012) resulted in a 10-35% relative change in survival for five of the six release groups in that study.” (p. 663) First, there is no basis to the assessment findings that Delta exports, already restricted in the December to June period, would be further restricted with WaterFix. Second, the assessment of the south Delta effects did not take into account the added stress of reduced inflow of Sacramento River water into the interior Delta because of WaterFix. NMFS qualifies its own conclusion: “The extent to which management actions such as reduced negative OMR reverse flows, ratio of San Joaquin River inflow to exports, and ratio of exports to Delta inflow affect through-Delta survival is uncertain.” “Uncertainty in the relationships between south Delta hydrodynamics and through-Delta survival may be caused by the concurrent and confounding influence of correlated variables, overall low survival, and low power to detect differences.” (p. 687)

NMFS concludes no adverse effects: “After reviewing and analyzing the current status of the listed species and critical habitat, the environmental baseline within the action area, the effects of the proposed action, any effects of interrelated and interdependent activities, and cumulative effects, it is NMFS’ biological opinion that the proposed action is not likely to jeopardize the continued existence of Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, Southern DPS of North American green sturgeon or destroy or adversely modify designated critical habitat for these listed species.” (p. 1111) The basis for these conclusions appears to be balancing of north Delta negative effects with south Delta benefits, as well as the adaptive management capability offered by WaterFix.

In summary, then:

  • NMFS has understated the potential effect of the WaterFix on salmon migration survival through the Delta and the potential to minimize tidal effects based on WaterFix’s proposed rules and commitments. “(I)n the May 2016 Revised PA, DWR committed to Delta habitat restoration at a level that RMA Bay-Delta modeling indicates could prevent exacerbation of reverse flows in the north Delta due to the PA by changing the tidal prism in the Delta (see Section 2.5.1.2.7.1.2 NDD Bypass Flows and Smolt Entrainment Analysis).” (p. 623)
  • NMFS has overestimated the potential benefits of changes in the south Delta.
  • Based on past experience, NMFS’s assumption that real-time management of Delta operations by DWR and Reclamation (USBR) can overcome potentially damaging conditions is unfounded.

Figure 4. Map of key north Delta flow measurement locations.
“A” is Sacramento River at Freeport.
“B” is Sutter-Steamboat Slough.
“C” is Sacramento River below outlet to Georgiana Slough.
“D” is Georgianna Slough.

Sometimes it doesn’t take a lot of water.

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In a May 29 post, I discussed how a small diversion of cold water from the West Branch of the Feather River sustains the Butte Creek spring-run Chinook salmon, the largest spring-run salmon population in the Central Valley. In a May 8 post, I described how the Shasta River, despite its relatively small size, produces up to half the wild fall-run Chinook salmon of the Klamath River. In both examples, it is not the amount of water, but the quality of the water and the river habitat that matters. In the former case, man brought water to the fish. In the latter, man returned water and habitat to the fish.

While both examples are remarkable given the relatively small amount of water involved, the relatively small restoration effort required on the Shasta River and the minimal effect on agricultural water supply make it almost unique.

Just take a look at the present late May 2017 hydrology of the Klamath River (Figure 1). There was only 140 cfs flowing in the lower Shasta River. At the same time, there was 25,000 cfs flowing in the lower Klamath, 2000 cfs in the upper Klamath below Irongate Dam, and 2000 cfs in the Scott River. What is different is that most of the Shasta flow is spring fed, some of which is sustained through the summer. Of the roughly 300 cfs base flow in the river in late May 2017, about 200 was from springs (Figure 2). By mid-summer, flow out of the Shasta River into the Klamath will drop to about 50 cfs, with agricultural diversions from the Shasta at about 150 cfs. October through April streamflow is generally sufficient to sustain the fall-run salmon population. Summer flows are no longer sufficient to sustain the once abundant Coho and spring-run Chinook salmon.

Figure 1. Lower Klamath River with late May 2017 streamflows in red. Note Shasta River streamflow was only 140 cfs near Yreka, California. Data source: CDEC.

Figure 2. Selected Shasta River hydrology in late May 2017. Roughly 150 cfs of the 300 cfs total basin inflow is being diverted for agriculture, with remainder reaching the Klamath River. Red numbers are larger diversions. The “X’s” denote major springs. Big Springs alone provides near 100 cfs. Of the roughly 100 cfs entering Lake Shastina (Dwinnell Reservoir) from Parks Creek and the upper Shasta River and its tributaries, only 16 cfs is released to the lower river below the dam. Red numbers and arrows indicate larger agricultural diversions. Up to 15 cfs is diverted to the upper Shasta River from the north fork of the Sacramento River, west of Mount Shasta.

Butte Creek Spring-Run Chinook Salmon

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Photo of adult spring run salmon in upper Butte Creek canyon in summer awaiting fall spawning. Source: California Department of Fish and Wildlife (CDFW).

Butte Creek supports the largest population of spring-run Chinook salmon in California’s Central Valley.1  The recovery of Butte Creek spring-run salmon is one of the few modern success stories in the Sacramento River watershed. Efforts to restore fish passage and river habitats over the past several decades have paid off quite remarkably, but those efforts are now in jeopardy due to the recent drought and impending changes in water management in the Central Valley and Butte Creek.2

Butte Creek drains a portion of the mountains southwest of Mt. Lassen, on the east side of the Sacramento Valley (Figure 1). The creek’s steep canyon and falls prevent spring-run salmon from passing upstream of Quartz Bowl Pool. Spring-run spawn in about 13 miles of creek downstream of Quartz Bowl from mid-September through October. The adults arrive in the spawning area from about March through May or June. They hold in the deep pools in Butte Creek over the summer until they spawn in the fall. Fall-run salmon ascend the creek on high flow events at any time from September through December. However, CDFW intentionally blocks fall-run from migrating upstream of Parrot-Phelan Dam (location T6 in Figure 1), in order to prevent fall-run from interbreeding with spring-run and from spawning on top of redds that spring-run have already created.

The Butte Creek spring run has increased over the past 30 (Figure 2) in response to extensive active management. The Central Valley Project’s Anadromous Fish Restoration Program and the CalFed Program funded and implemented many fish passage projects and habitat improvements, in cooperation with DFW and local landowners. These programs purchased key properties, screened water diversions, constructed fish ladders, and restored floodplain habitats. PG&E improved management of its DeSabla – Centerville Hydroelectric Project at the upstream end of salmon habitat, increasing flows in the upper seven miles of Butte Creek’s salmon habitat and implementing focused management of the cold water that the hydro project moves through canals from the West Branch of the Feather River into Butte Creek. management improvements. DFW jump-started the recovery of Butte Creek spring-run by stocking spring-run smolts from the Feather River Hatchery in Butte Creek in the mid-1980s. Over that past ten-plus years, PG&E has funded CDFW to closely monitor salmon in Butte Creek.3

I took a close look at the recruit-per-spawner relationship (Figure 3) to portray long-term trends and factors related to success. The key findings are as follows:

  1. There is a strong positive recruit-per-spawner relationship with strong time (year) component – recruitment has increased steadily over the years with the buildup of the population.
  2. Recruitment per spawner was stronger for brood years with good conditions during critical time periods: fall spawning for their parents, winter-spring rearing and emigration, and subsequent over-summering holding conditions prior to their spawning.
  3. The initial stronger runs in the mid- to late-1980s (1986, 1988, and 1989) were jump-started with the initial stocking of Feather River hatchery smolts from 1983-1985 and optimal migration, summer holding, spawning and rearing conditions in the very wet years in the 1982-1986 period.
  4. The runs were again depressed during the extreme drought years of 1990-1992, only to recover and expand in the 1993-1999 period of wet years.
  5. Recruitment in 1984, 1985, 1999, and 2008 likely suffered from redd scouring in late fall (Nov-Dec) floods of 1981-1983, 1996, and 2005 (Figure 4).
  6. Recruitment per spawner in 2015 was poor due to drought rearing and migration conditions in winter-spring 2013, poor ocean conditions in 2014-15, and poor adult migration and over-summering conditions in 2015. In contrast, the 2016 recruitment per spawner was much higher, likely because of better adult migration and over-summer holding conditions (the drought had broken in 2016).

Present management focuses on protecting over-summering adults, primarily by ensuring they have adequate cool water to sustain them until fall spawning. This is not possible without the cool water from the West Branch of the Feather River provided by the PG&E hydro project near Paradise, CA. The future of that project and the Butte Creek spring run salmon are now in limbo.

Figure 1. Butte Creek spawning and monitoring locations for spring-run and fall- run salmon. Spring salmon can reach as far upstream as Quartz Bowl (T1). CDFW intentionally blocks fall-run at the Parrot-Phelan Dam (T6). Juveniles emigrate from spawning grounds in Butte Creek to the Sacramento River (below T9) via Butte Slough, the Sutter Bypass canals, and various other natural and man-made channels in the Butte Sink, west of the Sutter Buttes Source: CDFW.

 

Figure 2. Escapement estimates (spawners) observed in the spawning reach of Butte Creek from 1975-2016. Source: CDFW GrandTab.

Figure 3. Recruit-spawner relationship for Butte Creek spring-run Chinook salmon (log10 transformed). Year noted is recruit year. Color red denotes dry year rearing (year two years before). Blue denotes wet year. Green is average or normal year. Conditions encountered during spawning can also affect recruit survival. For example high pre-spawn mortality can occur that detracts from escapement estimate. Examples include 1987, 1992, 2003, 2008, and 2015.

Figure 4. Mean monthly flows in Butte Creek as measured at Chico, CA. Daily flows were high – up to 4600 cfs in Nov-81 and 5000 cfs in Dec-81, and 11,000 cfs in Dec-05.

Shasta River Fall Run Chinook Salmon – Status and Future

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In an April 10, 2017 post, I described a sharp decline in the Klamath River salmon runs after the 2012-2015 drought. In that post, I also noted the high relative contribution of the Shasta River run to the overall Klamath run, especially in the past six years. The recent upturn in the Shasta River run and its greater contribution to the overall Klamath run is likely a consequence of efforts by the Nature Conservancy and others to restore the Big Springs Complex of the upper river near Weed, Ca.

The Shasta run has increased measurably since 2010 (Figure 1). Cattle were excluded from Big Springs Creek in 2009, and flows, water temperature and juvenile Chinook densities were markedly improved in and below Big Springs Creek.1 The improved juvenile salmon production likely contributed to greater runs from 2011-2015 and to a higher than expected 2016 run given the 2013-2014 drought (Figure 2). The improvement in the Shasta run bodes well for the Shasta and Klamath runs (Figures 3 and 4). The Shasta run recovery is key to sustaining and restoring the Klamath run and coastal Oregon and California fisheries that depend on the Klamath’s contribution. The Shasta River’s spring-fed water supply comes from the Mt. Shasta volcanic complex. This water supply is resilient to drought and climate-change. The reliability of the Shasta River’s water supply makes the Shasta River’s contribution to Klamath salmon runs particularly important.

Restoration of the Shasta River and recovery of its salmon and steelhead populations has only just begun. Further improvements to the Big Springs Complex, especially to its spring-fed water supply (Figure 5) and to its spawning and rearing habitat, are planned. There is also much potential to improve habitat above the outlet of Big Springs Creek, both in the Shasta River and Parks Creek. There is further potential for habitat restoration in downstream tributaries (e.g., Yreka Creek and Little Shasta River). Reconnection of the upper Shasta River above Dwinnell Reservoir to the lower river would restore many miles of historic salmon and steelhead producing habitat.2 These improvements could make it is possible for the Shasta River to once again produce over half the “wild” (non-hatchery) salmon of the Klamath River.

Figure 1. Fall-run Chinook salmon escapement (spawning run) estimates for the Shasta River from 1978 to 2016. Data Source: CDFW GrandTab.

Figure 2. Mean annual Shasta River streamflow (cfs) as measured at Yreka, CA. Source: USGS. Designated water-year types in this figure are the author’s estimates.

Figure 3. Spawner-recruit relationship for Shasta River. Escapement estimates (log10X – 2 transformed) are plotted for recruits by escapement (spawners) three years earlier. Year shown is recruit (escapement) year. The number is the year that fish returned to the Shasta River to spawn. The color of the number depicts the water-year type in the Shasta River during the year the recruits reared. The color of the circle depicts the water-year type in the Klamath River during the year the recruits reared. Blue is for Wet water-year types. Green is for Normal water-year types. Red is for Dry water-year types. Example: 90 depicts fish that returned to the Shasta River as adult spawners in 1990. These fish were spawned in 1987 and reared in winter-spring 1988. The red number shows that the 1988 rearing year was a Dry water year in the Shasta River; the red circle shows that the 1988 rearing year was a Dry water year in the Klamath River. Note very poor recruits per spawner in 1990-1993 drought period, compared with relatively high recruits per spawner from 2011-2016, even though the latter period included the 2012-2015 drought.

Figure 4. Estimates of fall-run Chinook salmon escapement for the Klamath River, 1978-2016. Data Source: CDFW GrandTab.

Figure 5. Examples of Shasta River monthly average flows as measured at the lower end of Shasta Valley. Streamflow is low from late spring through summer because of surface and groundwater irrigation demands. October flows are higher because the irrigation season (and season of diversion under some water rights) ends on September 30. Data source: USGS Yreka gage.

Scott River Fall-Run Chinook Salmon

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In an April 10 post on the Klamath Chinook salmon run, I discussed an expected record low run in 2017.  The Klamath run has six subcomponent runs, including the Scott River.  Improving the Scott River run is one means of improving the Klamath run.

Like the adjacent Shasta and Salmon Rivers, the Scott is a unique ecological gem, sitting high in the Marble and Trinity mountains before plunging north down the volcanic escarpment into the Klamath River canyon (Figure 1).  Like the Shasta River, the Scott flows through a mountain rimmed glacial valley not unlike those in the North American Rockies or European Alps.  Scott Valley is one of those “beautiful places.”  It is also one of the last great places for salmon and steelhead in California.  Unlike the Shasta River whose flow is supported by large volcanic springs from Mt. Shasta, the Scott depends on snowmelt from the Marbles and Trinities, as well as on springs from its alluvial valley.

Figure 1. The Scott River Valley in northern California west of Yreka, CA (Yreka is located in the Shasta River Valley). The Scott and Shasta Rivers flow north into the Klamath River, which runs west to the ocean. The Salmon River watershed is immediately west of the Scott River watershed. The upper Trinity River watershed is immediately to the south of the Scott River watershed.

The Scott River is home to wild runs of Chinook salmon, Coho salmon, and steelhead trout that make up significant components of the Klamath River runs of these species. In this post I address the Scott River fall-run Chinook salmon. The California Department of Fish and Wildlife has estimated the annual run size since 1978 (Figure 2).

Figure 2. Escapement of adult fall-run Chinook salmon to the Scott River from 1978 to 2016. Data source: CDFW GrandTab.

The run size, or “escapement” in fisheries science vernacular, is a consequence of the previous number of spawners; their success; survival of eggs, embryos, fry, and smolts in rivers; survival for up to several years in the ocean; and finally, the success of adults migrating back from the ocean to river spawning grounds. There is a lot that can happen at each of these life stages that may affect the ultimate escapement. I show the effect of several key factors in Figure 3, which starts from the escapement numbers in Figure 2 and shows the recruits-per-spawner relationship.

I hypothesized the following from the Figure 3 recruits-per-spawner relationship:

  1. Recruits-per-spawner is generally higher for wet (blue) rearing conditions – the winter/spring conditions of the year that followed the spawning or brood year. Note that smolts generally reach the ocean by their first summer, so conditions early in their rearing year likely affect survival prior to entering the ocean. Survival may be affected by the rearing conditions in the Scott River and/or those downstream in the Klamath River. Low late-winter and spring flows affect river rearing survival as well as the overall survival during emigration to the ocean. Ocean survival can be a consequence of success during river rearing or emigration: of the smolts that reach the ocean, larger healthier smolts generally survive better in the ocean.
  2. Recruits-per-spawner is generally lower as a consequence of dry conditions during the spawning run (red circle years have lower recruits-per-spawner). The lower Klamath River die-off of adult salmon in 2002 was an example of dry year mortality during the spawning migration.
  3. Recruits-per-spawner may be depressed in very wet rearing years when floods disturb spawning beds of salmon. An example is 1999. The number of recruits was depressed by the 1997 New Years flood, which affected the fall 1996 spawn. Similarly, floods in winter 1982, 1983, 1996, 1998, and 2006 may have reduced survival and run size in 1984, 1985, 1998, 2000, and 2008.
  4. The number of spawners three years earlier has little or no apparent effect on the number of recruits (at least at these levels of spawners). For example: recruits in 2007 and 2008 were relatively high despite low number of spawners three years earlier.

I derived the wet or dry water year designations using Figure 4. I derived the wet or dry August-September streamflow designations for the spawning run from the average monthly Scott River streamflow for those months and years (Figure 5 shows a sample range of years). Note that there is not a lot of difference among years in the August-October flows – they are all relatively low. That is because by August, the snow-melt season is over and base flows are occurring from springs and hay-field and pasture runoff or seepage.

There is also the negative effect on flows from wells and surface diversions, the predominate forms of irrigation in Scott Valley. In the drier years the late summer and early fall river flows exiting the Valley below Ft. Jones can be extremely low (less than 10 cfs – see Figure 5) because of extensive well use, driven by lower available surface water. Low late summer and early fall flows can block salmon from entering the river for several months (Figure 6). This results in loss of stored energy, lower egg viability, and high pre-spawn mortality. It also results in delayed spawning, increasing the likelihood that salmon will spawn in the lower sections of the Scott River, where there is poor spawning and rearing habitat. Low flows in the river upstream can further hinder migration and access to prime spawning tributaries (Figure 7).

It takes about 100 cfs or higher to provide full access to the upper river’s spawning areas. In most years, flows are too low to provide good access. The Scott River Water Trust purchases irrigation water in some years to help the salmon migration. In most years, the river’s baseflows increase soon after the irrigation draw on groundwater ends in late October, allowing unhindered migration.

Part of the solution to the problem of low flows during the spawning run is to cease irrigation earlier. Hay irrigators generally cease pumping water by October 1, and some say there is minimal benefit of irrigating after August. Ranchers often irrigate pastures into November, if only for stock watering. Because many wells are not operated after August, idle wells have sufficient total capacity to readily keep the river watered after September 1 to pump groundwater directly into the river (ranchers would consider this if the costs of pumping were covered). I believe the effect of the extra pumping on groundwater levels would be minimal, because the Valley aquifer recovers from well pumping over the winter-spring recharge season.

Survival during the late winter-early spring rearing and emigration period could be enhanced in drier years by limiting early spring irrigation use and using selected idle wells prior to the irrigation season to add water directly to the river.

In summary, the Scott Chinook fall-run is reduced in dry years when spawning and rearing success are compromised by low river flows in the Scott and Klamath Rivers. The Scott River Chinook salmon population would likely benefit from (1) improved late-summer and early-fall flows that would improve access of spawners to upriver and tributary spawning grounds, and (2) higher river flows in drier years during the late–winter and early-spring rearing and emigration period. A record low run is expected in fall 2017 because of low fall and spring flows in 2015, which limited the survival of the juveniles from the 2014 run.

Figure 3. The recruit-per-spawner relationship for the Scott River fall-run Chinook salmon from 1978 to 2016. Escapement by year (recruits) is plotted against escapement three years earlier (spawners). The escapement values plotted are transformed (Log10X-2). The number shown is the escapement year or recruit year – the year the run was tallied. Number color denotes rearing year water supply type – two years prior to recruit year. Red is dry. Green is average. Blue is wet. Circle represents escapement year water supply during the spawning run (August-September). For example: “04” is run size in fall 2004, which had an average winter-spring rearing year (water year 2002) and dry conditions during the late summer run in 2004 (red circle).

Figure 4. Water years (10/1-9/30) 1978-2016 average annual flow in Scott River measured at Ft. Jones gage. Source: USGS. I designated years above the blue line as wet years, years below the red line as dry years, and years between the lines as average years.

Figure 5. Scott River average monthly flow (cfs) below Ft. Jones for selected years. Source: USGS.

Figure 6. Adult fall-run Chinook salmon waiting at the mouth of the Scott River in the Klamath River in late summer for flows to improve before attempting to migrate up the Scott River to their spawning grounds.

Figure 7. Trickle of flow in the mainstem Scott River in Scott Valley during late summer below Young’s Dam irrigation diversion near Etna, CA. The dam can be seen in the distance at upper center of photo. The fish ladder at the dam is not functional at such low flows. The dam is located approximately 50 river-miles upstream from the river mouth. There is approximately 20 miles of additional Chinook salmon spawning habitat upstream of Young’s Dam.