Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Salmon and Smelt Shorted in 2017

Posted on by

The Northern California Water Association stated on September 14: “For the better part of three decades, greater and greater quantities of water were dedicated to instream flows with the expectation that this “silver bullet” of flows, on its own, would solve the diverse assortment of fish mortality causes. The result, on the rivers and streams where this was the primary or only action used to promote survivability, was generally unproductive.” This statement is so misleading and untrue. It is outright propaganda. Streamflow is absolutely necessary to maintain salmon, steelhead, sturgeon, and smelt throughout the Central Valley, and reductions in streamflow have been directly related to fish mortality and population abundance.

The truth is that each year the state and federal water projects in the Central Valley keep squeezing more and more water from the system. There is no better example than in 2017, a near record water and snowpack year. Even in this very wet water year, water managers are saving water for use in future years rather than applying it as required for the fish. Their excuse is that they must save the water to preserve the cold-water pool in Shasta reservoir for the summer and fall salmon spawn. While that is a true need in drier years, it is not in wet years when Lake Shasta fills.

Water users got full allocations this year. Delta exports reached a near record 6.2 million acre-feet (MAF) of water in Water Year 2017. So instead of keeping river flows up to meet salmon needs with water that users did not need, project managers saved the water for next year’s use. While saving Shasta storage for next year is not a bad thing, saving this year’s fish water for next year’s contractor allocations is certainly not good for fish species near extinction.

How is the fish water saved? The basic approach is to limit Shasta releases and violate fish water temperature standards in the 200-miles of the Sacramento River down to the Delta. The standards require maintaining spring-to-fall water temperature at Red Bluff at 56oF and at 68oF between Red Bluff and the Delta. It takes releases of cold water from Shasta to maintain the Red Bluff standard. In the lower river, it is the flow rate that maintains the standard. With Sacramento River contractors receiving their full allocations and the Delta diverters getting all the water they needed in 2017, there was an overt effort to save the water in Lake Shasta at the expense of the salmon.

The water managers and resource agencies started by moving the Red Bluff 56oF standard compliance point upstream 33 miles to Balls Ferry, leaving over half the upper 60-mile salmon spawning reach without protection. That action is for dry years, not wet years. The combination of lower and warmer Shasta/Keswick releases resulted in excessively high water temperatures near Red Bluff (Figure 1). Lower Shasta releases and lower flows below Red Bluff led to low flows and high water temperatures 120 miles downstream at Wilkins Slough during the summer (Figure 2). By ignoring the water temperature standards, water managersheld approximately 300 thousand acre-feet (TAF) of extra water in storage at Lake Shasta (the amount in yellow area of Figure 2). The standards were also exceeded 40 miles further downstream at Verona (Figure 3); again, the amount that would have been necessary to maintain the standard was about 300 TAF. The effect translated to higher water temperatures 30 miles further downstream in the Delta at Freeport (Figure 4).

Was the 300 TAF of storage saving necessary to preserve Shasta’s cold-water pool to protect salmon in the upper river spawning area over the summer and into the fall? No, and certainly not at the expense of salmon, steelhead, sturgeon, and smelt over the summer in the river, Delta, and Bay. First, there was sufficient cold water to maintain the standards through the summer, regardless what the agencies say or their models predicted. There was 400 TAF more water in the Shasta cold-water pool than in 2016 (Figures 5 and 6). Standards had been maintained in the two previous wet years, 2006 and 2011. Had water managers released the water for fish in 2017, the end-of-September storage would have been 3.1 MAF instead of the projected 3.4 MAF. The 3.1 MAF is adequate and within project goals. It is twice the end-of-September storage of 2015, and 10% higher than 2016. Second, if the 300-TAF was too high a price, some or all of it could have been allocated from the over 8 MAF of water diverted from the Sacramento River and the Delta for water use. Third, if a shortage of the cold-water was a concern, less warm water from the Trinity-Whiskeytown trans-basin diversion could have been delivered to the Sacramento River, or less peaking hydropower generation at Shasta Dam could have occurred: both are known factors in cold-water pool depletion.

In summary, water project managers in the Central Valley saved 300 TAF by not meeting water temperature standards for the Sacramento River in summer 2017. In the whole scheme of 2017 water management it seems “small potatoes” (Figure 7), but maintaining the long-held standard is important for salmon. There was no valid excuse for not meeting the water temperature standards. Salmon, steelhead, sturgeon, and smelt suffered unnecessarily from the violation of the water temperature standards.

Figure 1. Summer 2017 water temperature in the Sacramento River at Red Bluff (RM 243). Red line denotes 56oF water temperature standard necessary to protect spawning salmon, steelhead, and sturgeon. (Base chart source: CDEC)

Figure 2. Summer 2017 water temperature at Wilkins Slough (Sacramento River at RM 125). Multiple temperature lines indicate daily highs and lows. Red line is the 20oC (68oF) standard. Yellow area is the roughly 300 TAF that was saved by not meeting the standard (maintaining about 7000 cfs). (Base chart source: USGS)

Figure 3. Summer 2017 water temperature at Verona (Sacramento River at RM 80). Multiple temperature lines indicate daily highs and lows. Red line is the 20oC (68oF) standard. Yellow area is the roughly 300 TAF that was saved by not meeting the standard (maintaining about 17,000 cfs). (Base chart source: USGS)

Figure 4. Summer 2017 water temperature at Freeport (Sacramento River channel in north Delta). Multiple temperature lines indicate daily highs and lows. Green line is the flow that would have occurred to maintain upriver water temperature standards. Yellow area is the roughly 300 TAF that was saved by not meeting the standard. Had this water reached the Delta and Bay it would have benefitted Delta smelt by keeping the Delta cooler and maintaining the low salinity zone further downstream in the Bay. (Base chart source: USGS)

Figure 5. Water storage and temperature distribution profile in Lake Shasta in 2016. (Source: USBR CVO)

Figure 6. Water storage and temperature distribution profile in Lake Shasta in 2017. (Source: USBR CVO)

Figure 7. Water Year 2017 flows in the Sacramento River at Wilkins Slough. Near 300 TAF of Shasta storage was saved by reducing flows below the norm in summer (red circle). Base chart source: USGS.

Fall Smelt Protections Removed

Posted on by

On September 28, the US Fish and Wildlife Service (Service) approved removal of fall protections for Delta smelt that have been in place since 2008. The action allows south Delta pumping plants to export an additional 400,000 acre-feet of water on top of the 6.2 million acre-feet already exported through September in Water Year 2017. The water, earmarked for the Bay and Delta smelt, instead will go to southern California to fill reservoirs.

The action allows X2, the 2 parts per thousand salinity prescription, to be moved from Chipps Island (river kilometer 74) upstream to Collinsville (river kilometer 81). The action occurs simply by increasing south Delta exports, keeping all other factors constant (Figures 1 and 2). Exports have risen from 8,000 cfs to the maximum of 11,700 cfs. Delta net freshwater outflow to the Bay has fallen from 15,000 cfs to 10,000 with the higher exports and slowly falling Delta inflow (Figure 3). Salinity at Collinsville has nearly reached its new allowed level (Figure 4).

The effects of the higher exports can be seen in flows measured in Old River in the central Delta near Highway 4 (Figure 5). Flows through nearly the entire tidal cycle are negative as water rushes to meet the maxed-out exports in the south Delta. The daily average, also called OMR, is -5,000 cfs. Other channels, including the lower San Joaquin River, make up the remainder of the 11,700 cfs level of export.

The Service concludes that “the proposed Fall X2 action for 2017 would not adversely affect Delta Smelt” P5. They state that they see no evidence that the change will affect the smelt population. This is an incredible conclusion given the present state of the population (Figure 6). There is simply no basis for the conclusion other than saying the smelt are all gone anyway.

Reductions in Delta outflow, upstream movement of X2 into the western Delta, and negative net flows in any Delta channel are a direct and real threat to Delta smelt and their habitat (as the Service points out in its approval letter on page 8). In Reclamation’s request for the action, Reclamation frames the issue an adaptive management action within the context of the original 2008 biological opinion prescription. With the species on the brink of extinction, such negative “adaptive management” actions are not the logical approach to be taken toward recovery of the species. The prescription allowed adaptive management actions to help toward recovery, not to top off southern California reservoirs.

Sad thing is, 2017 is only the second year with hydrological conditions applicable to the 2008 fall X2 prescription. In 2011, the first and now only application of the prescription, the fall X2 requirement proved to contribute significantly toward recovery, as shown in the Fall Midwater Trawl Survey. I suspect there will be no similar “bounce” in the October-through-December survey index in 2017.

Figure 1. Tracy (federal) exports in September 2017.

Figure 2. Clifton Court (state) exports in September 2017.

Figure 3. Delta outflow to Bay in summer 2017.

Figure 4. Salinity (EC) at Collinsville (river kilometer 81) in September 2017.

Figure 5. Hourly flow in cfs in Old River in central Delta near Highway 4 crossing.

Figure 6. Delta smelt summer townet index 1969-2017. (CDFW data).

Figure 7. Fall midwater trawl index for Delta smelt

Webber Lake

Posted on by

Webber Lake is a natural Sierra lake at 6500’ elevation north of Truckee. Located in the Little Truckee River headwaters, it was recently purchased and opened to the public by Tahoe-Donner Land Trust.1

Webber Lake was once renowned for big trout (privately stocked), but it is now a put-and-take fishery with a few holdovers (standard trout fishing regulations). The lake so far has no milfoil (boats and float tubes must be “certified” by staff). It has nice pond weed beds with abundant red shiners. It is a relatively small but deep (> 40’). The lake and valley are very quiet and pristine. Eagles, osprey, terns, and cranes are common.

The lake is situated off Hwy 89 on the way to Portola in a serene mountain valley. The adjacent mountains still have late summer patches of snow. It has a nice campground ($30; 35 widely spaced sites in woods next to lake) and day-use parking area (no fee). An RV camp will open next year.

The fishery is now managed by CDFW with mostly small 8-inch planter rainbow trout and holdovers from prior years’ stocking. I have not heard of any recent catches of browns or brookies, though in the past both were commonly stocked. Natural spawning creeks that can support wild trout flow into the lake.

It is sad to see this natural gem managed as another put-and-take trout lake like most of its neighbors (Davis, Frenchman, Gold, Boca, and Stampede, etc.). It could be managed as a wild trout lake, on the model that the Nature Conservancy now manages nearby Independence Lake.2 DFW has recently started stocking Webber Lake with Lahontan cutthroat, the native trout of the Truckee watershed. This suggests that management of the lake for wild native trout might be considered in the future.

WaterFix NMFS Biological Opinion Conclusions on Salmon in the Delta

Posted on by

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.

The Twin-Tunnels Project: Effects on Upper Sacramento River Salmon Habitat

Posted on by

The NOAA 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 the upper Sacramento River salmon, steelhead, and sturgeon in the upper 60 miles of river between Keswick Dam in Redding downstream to Red Bluff.

This is one in a series of posts on the WaterFix. Within that series, it is the first post of the series on the NMFS BO. In this series within a series, I focus on what NMFS determined from its review and the veracity of its conclusions about effects. I pose and respond to the following questions: Will the WaterFix change reservoir storage and release patterns, water temperatures and flow patterns. Will the WaterFix change the rates of survival of Sacramento River salmon, steelhead, and sturgeon? Will changes affect survival and contributions to sport and commercial fisheries?

The Sacramento River between Keswick Dam and Red Bluff is spawning and early juvenile rearing habitat for all four races of salmon, including the listed winter-run and spring-run, and for green sturgeon. All of these species depend on cold-water flows from Shasta reservoir. Winter-run salmon survival was poor in the reach in 2014 and 2015,1 as well as in past droughts when the cold-water supply ran out.

Will conditions improve or get worse with the WaterFix? The NMFS assessment concludes that conditions will worsen with WaterFix only in critically dry years like 2014 and 2015, and possibly in below normal water years. Because such poor survival years are the cause of historic population crashes, it is hard to understand how NMFS concludes that making such years worse is not a worry, or even “jeopardy.”

The NMFS analyses rely on model predictions that NMFS admits are crude, with monthly inputs and outputs. Rules that govern the models are subject to change. In the end, NMFS simply states that adaptive management will protect the salmon in all but critically dry years. The BO makes no attempt to prescribe new rules that would be more protective.

The real concerns about WaterFix are: (1) whether the new Delta export capacity will place new demands on Shasta storage within and among years; (2) whether seasonal flows and water temperatures will change; and (3) whether changes in storage, flows and temperatures will affect salmon, steelhead, and sturgeon.

I really did not get a sense from the BO (or from the EIR/EIS or the Biological Assessment) how WaterFix would be operated. With the extra diversion capacity in the Delta (under the prescribed WaterFix rules for diversions in the Delta), would the Bureau of Reclamation (BOR) or the Department of Water Resources (DWR) release more water from storage in Shasta or Oroville or Folsom to achieve greater south-of-Delta exports under some circumstances? How would they know how much “new” water could be taken, and whether that water would compete with other demands, even from the proposed Sites Reservoir. If they miscalculated the extent of the Shasta cold-water pool in 2014 and 2015, what measures would they take to protect the cold-water pool with the new WaterFix capacity? Would they drain more of Shasta than under present demands? There are lots of questions not posed and not answered.

Excerpts from the NMFS BO, Section 2.5.1.2.

“This preliminary analysis indicated that there is the potential for changes as a result of the PA (WaterFix) in reservoir operations, in stream flows, and water temperatures in the Sacramento River and American River. Therefore, this section assesses potential effects of those changes on listed aquatic species and critical habitat in the American River and Sacramento River upstream of the Delta.” Comment: An example plot from the analyses is shown below. NMFS implies that these are model anomalies and not real. Years 2012 and 2016 were below normal years and represented by the Figure. What did the models assume to create these significant effects? Would WaterFix take more or less water?

PA is WaterFix; NAA is No Action Alternative.

“Existing Biological Opinions on the Long-Term Operations of the CVP and SWP, NMFS and Reclamation are considering modifications to the RPA relating to Shasta Reservoir operations”. Comment: Like many aspects of WaterFix, other regulatory processes could change the rules. Some changes yet to occur could significantly change the amount of water available for WaterFix.

“Under dual conveyance of the Proposed Action (PA), reservoir water releases and, therefore, CWP [Shasta cold-water-pool] availability may be changed from existing conditions for optimization of exports in the north and south Delta. If CWP storage and management is improved or degraded it could have effects on the viability of listed salmonids.” Comment: Ominous uncertainty for a biological opinion.

“ [T]he extent of habitat cold enough for spawning and early life stage survival changes every year in relation to where in the Sacramento River the upper temperature threshold of 56°F (13.3°C) can be maintained from May to October.” Comment: This is one of the rules that has so easily been changed without adequate review or process. It is one rule that can change to benefit WaterFix water supply.

“Under dual conveyance of the Proposed Action (PA), reservoir water releases and, therefore, CWP availability may be changed from existing conditions for optimization of exports in the north and south Delta. If CWP storage and management is improved or degraded it could have effects on the viability of listed salmonids.” Comment: Incredible uncertainty. There are minimal constraints built into the WaterFix. The conflict between fish and water exports will be more extreme than ever before.

“Recently, a succession of dry years with low precipitation highlighted how difficult the upper river spawning area is to manage for successful spawning and embryo incubation. High mortality (greater than 95%) in the youngest life-stages (eggs, yolk-sac fry) resulted when temperature compliance points were not maintained under 56°F (13.3°C) for the spawning and embryo incubation season (Swart 2016).” Comment: The risks are obvious. Difficulty cannot be an excuse for poor management.

“Green sturgeon have different temperature requirements than salmonids in the upper Sacramento River. The majority of green sturgeon spawn above Red Bluff Diversion Dam. Suitable spawning temperatures must remain below 63°F (17.5°C) to reduce sub-lethal and lethal effects. Temperatures in the range of 57° to 62°F (14 to 17°C) appear to be optimal for embryonic development (Van Eenennaam et al. 2005).” Comment: The assessment on green sturgeon is almost non-existent. The optimal conditions are already exceeded upstream and downstream of Red Bluff in the spring season when sturgeon spawn.

Salmon Conclusions from the NMFS BO

“A high proportion of developing embryos are expected to perish from exposure to lethal water temperatures in critically dry water years.” (p. 279) Comment: This can be reasonably avoided and should not be “expected” or accepted.

“Mean annual temperature-dependent survival would decrease under the PA by 1% in wet years and 3% in below normal years.” (p. 281) Comment: Such predictions from the models are meaningless. Risks to salmon remain serious and are readily avoidable with effective controls.

“All differences in mean annual temperature-dependent survival are likely within the margin of error of the model and are not significant.” (p. 281) Comment: This is true only for the crude model predictions, but not for real risks from WaterFix.

“The SWFSC model results suggest that winter-run Chinook salmon egg survival will largely be the same under the NAA and PA operations.” (p. 282) Comment: Again, this applies to crude model predictions, not to real risks, which are significant given past management, operational rules, and regulatory constraints.

“Overall, the certainty of the three biological tools’ respective ability to accurately estimate thermal impacts to eggs and alevins in the Sacramento River under the PA is low because all three models utilize daily (thresholds analysis and the SWFSC’ egg/alevin mortality model) or weekly (SALMOD) water temperatures downscaled from the same modeled monthly values. Eggs and alevins developing in the Sacramento River spawning gravels experience a thermal regime that varies between day and night and from one day to the next. The downscaled water temperature modeling utilized in all the biological models does not capture that level of thermal variation. Nevertheless, the biological models are useful qualitative indicators of potential thermal impacts under the PA.” (p. 282) Comment: This says it all. The potential risks to salmon and sturgeon from WaterFix are real, unlike the model predictions.

“Adverse thermal effects on these life stages resulting from changes to upstream operations as a result of the PA are not expected. However, for purposes of the analysis in Section 2.7 Integration and Synthesis, the combined effect of PA implementation when added to the environmental baseline and modeled climate change impacts is expected to result in substantial water temperature-related mortality in critically dry years.” (p. 282) Comment: Again, the worst problems for salmon and sturgeon for decades have been in the critical dry years in drought sequences. WaterFix will do little to alleviate the problem, and will likely make it worse.

“There are extensive real-time operations management processes currently in place for CVP/SWP operations that affect water temperatures upstream of the Delta (see BA Section 3.1.5.1 Ongoing Processes to support Real-Time Decision Making), those processes have minimized such impacts in the past (Swart 2016), and the PA does not propose changing the existing real-time operational processes. Therefore, NMFS concludes that the real-time operations management process would minimize adverse effects indicated in the modeling for the PA to a similar extent as the real-time operations process has minimized such impacts in the past.” (p. 282) Comment: Incredible statement. Past poor real-time management has led to the near extinction of winter-run. Even the extremes of 2014 and 2015 were avoidable if management had been effective. Yet WaterFix proposes no changes in management.

“NMFS expects that climate conditions will follow a trajectory of higher temperatures beyond 2030. Not only are annual air temperatures expected to continue to increase throughout the 21st century, but the rate of increase is projected to increase with time. That is, in the early part of the 21st century, the amount of warming in the Sacramento region is projected to be less than it is in the latter part of the century under both low and high carbon emissions scenarios (Cayan et al. 2009). Because water temperatures are influenced by air temperatures, NMFS expects that climate change will amplify adverse thermal effects of the proposed action combined with the environmental baseline and modeled climate change past 2030.” (p. 283) Comment: With future climate change, operations under WaterFix will likely create significant added risks to salmon, steelhead, and sturgeon.

Some Final Thoughts

While it is possible that the WaterFix would cause few changes in reservoir management upstream of the Delta, WaterFix is likely to increase demands at times on that storage, with many potential ramifications. The NMFS BO does not address any such changes and the rules that might limit them. Rules could even become more stringent to protect salmon and sturgeon, thus potentially reducing the water supply benefits of the WaterFix. But without operational constraints for reservoirs and other aspects of WaterFix, there is no basis for NMFS to state in a BO that it has predicted and mitigated the effects of the WaterFix on salmon, steelhead and sturgeon.

Finally, I have seen no suggestions to use WaterFix to improve upon existing Central Valley water operations to benefit salmon. For instance, WaterFix should make it possible to adjust some water demands to allow better management of Shasta’s cold-water pool. For now, WaterFix would seem to be just another tool to exploit the water resources of the Sacramento River system at the expense of salmon, steelhead, and sturgeon.