Mormon Crickets and Pikeminnow

When settlers moved into the desert west a century or so ago and started irrigating crops, they created new habitats for some species that Mother Nature had held in check. Species such as Mormon Crickets became pests, overwhelming the irrigated crops produced in the unnatural habitats and plaguing their human guests.1

The same goes for the Sacramento pikeminnow. The dams and farmland reclaimed from wetlands in California’s Central Valley have created ideal habitat for the pikeminnow. Pikeminnownow have become so abundant they have become predator nuisances that feed on ever-decreasing numbers of young salmon and steelhead. Pikeminnow also migrate from the Delta to spawn in valley rivers below dams where they prey on young salmonids. Juvenile pikeminnow compete with young salmonids for aquatic insects and feeding territory.

The problem also occurs on the Eel River, a large coastal salmon river that once featured some of the largest salmon and steelhead runs in California.2 Sacramento pikeminnow are not indigenous to the Eel River: they were introduced by anglers who brought “minnows” to use as bait to fish for trout stocked in PG&E’s Lake Pillsbury on the Eel River’s mainstem.

There are three ways to deal with the pikeminnow problem. One is to selectively eradicate them. The Columbia River water folks tried this first approach for decades now – that has not worked.3 The Eel River folks are trying weir traps.4

Another approach is to reduce the habitat conditions that allowed enables the high production of pikeminnow in the first place. Replacing warm, slow-moving pools with colder, faster-moving water makes habitat less conducive to pikeminnow.

A third approach is allowing salmon and steelhead to get to places the pikeminnow are not. Many organizations are seeking the removal of Scott Dam, which creates Lake Pillsbury. This will allow salmon and steelhead access to the Eel River upstream of the current lake. There are natural barriers upstream that steelhead and salmon can pass but that pikeminnow, which are weaker swimmers, cannot.

To help recover our native salmonids in the Central Valley, a combination of weirs and colder water, reverse engineering the habitat to reduce pikeminnow production, and the reintroduction of salmonids in higher elevations too cold for pikeminnow could be the recipe for success.

Cache Slough Tidal Wetland Restoration – Update More misguided resource-damaging habitat restoration for an already highly altered and compromised Delta

Cache Slough Complex Restoration

The Cache Slough Complex is in the lower (southern) Yolo Bypass in the north Delta region (Figure 1). It is the focus of the state’s tidal wetland restoration EcoRestore Program that spans 16,000 acres in the Cache Slough region of the Sacramento-San Joaquin Delta.

The 53,000-acre Cache Slough Complex is located in the northwest corner of the Sacramento-San Joaquin River Delta in Solano and Yolo counties (Figure 1). The Yolo Bypass receives inflow directly from the Sacramento River (Fremont Weir), the Colusa Basin Drain, Putah and Cache creeks, and agricultural and municipal discharges. The Cache Slough Complex exits the Yolo Bypass via Cache Slough, first connecting to the outlets of Miner and Steamboat Sloughs, before entering the tidal Sacramento River channel near Rio Vista.

The Cache Slough Complex has been identified as an area with great potential for tidal restoration as a result of its connectivity with the Yolo Bypass floodplain, suitable elevations, high turbidity, high primary and secondary productivity, and use by Delta smelt (Hypomesus transpacificus), Chinook salmon (Oncorhynchus tshawytscha), and other native fishes. Both federal and state wildlife agencies consider the Cache Slough Complex to be a prime area to advance habitat conservation to benefit endangered species in the Sacramento-San Joaquin Delta and incorporate improvements to the regional flood management system.

The latest project approved for construction is the Lookout Slough Project, a 3000-acre tidal marsh restoration immediately to the west of Liberty Island. The Project was certified by DWR in 2020 as mitigation/compensation for the Delta Tunnel Project. The Delta Stewardship Council recently denied appeals1 to the state’s certification of the Lookout Slough tidal marsh restoration project. Once completed, Lookout Slough will be the Delta’s largest single tidal habitat restoration project to date.

The Problem

Most of the tidal “restoration projects” in the Cache Slough Complex involve breeching leveed tracts of agricultural land to create subtidal or intertidal habitat. Tidal waters once confined to narrow floodplain channel are now allowed to pour through breaches onto over 10,000 acres of formerly diked farmlands. The process started between 1980 and 2000 when Little Holland Tract (1456 acres) and Liberty Island (4340 acres) levees failed and were not repaired, leaving these lands open to the tides. Because these reclaimed wetlands had subsided during active farming, most of the “restored tidelands” became sub-tidal, year-round, warm, shallow, open-water habitat. Such habitat is too warm for Delta native fishes except during the winter.

The enhanced tidal exchange and warm productive winter and early-spring habitat attracts migratory Delta native fishes like smelt, splittail, and salmon to the Cache Slough Complex. While such habitat is considered beneficial in winter, it warms excessively in spring and summer, reducing the period of quality rearing, and can reduce overall survival and production. Native fishes have succumbed to the heat, stranding in the uneven landforms, and predation by non-native warm-water fish.

The latest projects, Lower Yolo Ranch (1749 acres), Yolo Flyway Farms (300 acres), and Lookout Slough (3000 acres), will add 5000 acres of mostly shallow intertidal habitat. Tidewater will flood onto these lands twice a day to warm in the California sun and then return to cooler deep, shaded, sub-tidal sloughs long considered prime Delta smelt and salmon rearing habitat. Not only will the new inter-tidal “wetlands” be too warm, but they will contribute to warming adjacent sub-tidal sloughs that convey water to and from other parts of the north Delta. This water quality degradation gets worse with each new project and has resulted in the degradation of the entire north Delta as a viable spawning, rearing, and critical habitat of Delta smelt. The effect has measurably contributed to the near extinction of Delta smelt.

The Evidence

The United States Geological Service has many water quality and flow monitoring gages in the Cache Slough Complex (Figure 2) that provide considerable evidence of the above-described problem. Specific gages with pertinent data records reviewed for this post are highlighted in Figure 2.

Waters in the northern Cache Slough Complex become too warm for salmon and smelt (>20ºC) by spring (Figure 3). In summer (Figure 4), water tidally flooded into subtidal island-tracts can warm 5-7ºC over a day before draining back into adjacent sloughs. Water temperatures in the northern sloughs of the Cache Slough Complex reach 25ºC (lethal to smelt) or higher in summer, even in wet and normal water years (2016-2018, Figure 5). Water temperatures in the southern Cache Slough Complex are only slightly lower (Figure 6). Over the past decade, water temperatures in the Cache Slough Complex overall have been gradually increasing (Figures 7 and 8), to the detriment of Delta native fishes.

The Solution

The problem can be lessened or even reversed at existing and future restoration projects by:

  1. Limiting tidal access to sub-tidal sites to winter, when water and air temperatures are colder.
  2. Building projects with flow-through tidal channel features rather than a single opening.
  3. Ensuring that projects are inter-tidal with small, narrow, shaded channels, or tule benches.
  4. Narrowing, deepening, and shading connecting tidal sloughs.
  5. Limiting discharge of warm agricultural wastewater into tidal channels.
  6. Providing supplementary inflow of Sacramento River water from the Fremont Weir, from the entrance gates of the Sacramento Deepwater Shipping Channel, or from other locations.
  7. Retrofitting existing restoration sites and designing future projects as outlined above.

 

Figure 2. USGS gage locations in the Cache Slough Complex.

Figure 3. Water temperatures recorded at Little Holland Tract in 2015-16.

Figure 4. Water temperatures and water surface elevation (gage height) recorded at Little Holland Tract in July 2017. Note higher water temperature spikes occurred with strongest ebb (draining) tides.

Figure 5. Water temperature in Liberty Cut adjacent to Little Holland Tract, 2016-18.

Figure 6. Water temperature and tidally-filtered flow rate in Sacramento Deepwater Ship Channel, April-September 2021.

Figure 7. Water temperature in lower Cache Slough, 2011-2016.

Figure 8. Water temperature in the lower Sacramento River channel near Rio Vista, 2010-2019.

Yolo Flyway Farms Tidal Wetland Restoration Project

Yolo Flyway Farms

The Yolo Flyway Farms project is a new element of the state’s EcoRestore program to fulfill requirements of federal biological opinions for the State Water Project and Central Valley Project. The 300-acre tidal wetland restoration project is located in the southern Yolo Bypass in what is commonly referred to as the Cache Slough Complex (Figure 1). The Project’s design entails allowing tidal access to excavated upland irrigated pasture land by opening levees along Prospect Slough (Figure 2). The Project is in a known area of concentration for Delta smelt as determined by nearby CDWR screw trap sampling in Prospect Slough (Figure 3). Project sponsors submitted a certification of consistency with the Delta Plan to the Delta Stewardship Council.1

Are such projects in the best interest of the Delta smelt population? A close look at project attributes may help answer the question.

Positive attributes:

  1. Replacement of the existing tide gate irrigation system with open levee breaches eliminates existing entrainment and loss of Delta smelt and other fishes into the irrigated pasture lands.
  2. New tidal channels and tidal wetlands would provide rearing habitat for young smelt, salmon, and splittail. Plankton and benthic invertebrate food sources for fish would likely increase.
  3. Hard surfaces may provide smelt spawning habitat.

Negative attributes:

  1. Tidal channels would provide new habitat for predatory birds and fish , which could increase loss of young smelt and salmon. Prospect Slough is deep, turbid, strong- current habitat unfavorable to predators. Tidal channels of project would be dead end, low velocity, less turbid habitats favorable to predators of fish.
  2. The southern Yolo Bypass aquatic habitats are warm from spring through fall, at times exceeding the thermal optimum for Delta smelt. Proposed shallow-water dead-end sloughs and flooded wetlands would warm and increase warming of Prospect Slough and other lower Bypass waters. While a positive attribute in winter and at times in late fall and early spring, this would be detrimental at other times.

Despite the potential positive benefits of such restoration in general, the potential negative aspects of the Project are a real concern. Some of the potential negative effects could be reduced through changes in project design and operations. At a minimum, the project should be considered an adaptive management experiment where potential positive and negative attributes are studied to determine the overall benefit of the action and whether it fulfills the objectives of the biological opinions.

Figure 1. Yolo Flyway Farms Project location (red circle) in southern Yolo Bypass.

Figure 3. Prospect Slough adjacent to Deepwater Shipping Channel and Liberty Island in southern Yolo Bypass. CDWR screw trap in yellow circle.

Yuba River Salmon in 2022

In a December 2020 post, I described the status of the fall-run salmon population in the Yuba River.  Hatchery salmon predominate, while natural production is minimal.  The population remains in a very poor state – at about 10% of recent historical levels during and subsequent to multiyear droughts such as 2007-2009 and 2013-2015 (Figure 1).

In a January 11, 2022 post, the South Yuba River Citizens League (SYRCL) promotes cleaning the two fish ladders at Daguerre Dam half way up the river to the impassable Englebright Dam, in order to provide better passage for spawning salmon to prime spawning habitat.  Without effective ladders, salmon are delayed or even forced to spawn downstream of Daguerre Dam in marginal habitat.  The ladders must be maintained per the federal NMFS biological opinion and take permit to operate Daguerre Dam as a water diversion dam for the Yuba County Water Agency (YCWA).

SYRCL’s plea to clean the fish ladders is helpful in bringing attention to the problems facing salmon (and steelhead) in the lower Yuba River.  However, the fish ladders at Daguerre are only a small part of the problem for Yuba River salmon.  River flows and habitat in the lower Yuba River need improvement.

River Flows

It is instructive to compare flows in 2020 (Figure 2) to flows in 2021 (Figure 3), particularly at the Marysville gage, where water has passed downstream of all the local agricultural diversions at Daguerre Dam.

2020

From May through mid-August of 2020, flows at Marysville averaged about 1000 cfs (Figure 2).  The vast majority of this water was released through YCWA’s New Colgate Powerhouse upstream of Englebright Dam.  In the fiscal year from July 1, 2020 to June 30, 2021, YCWA had revenues from power sales of over $80 million. 1 Water released during the summer creates more power revenue than flows released in spring.

Better management for fish would release more of the water in the spring, providing more areas in the lower Yuba River for juvenile salmon and steelhead to grow and higher flows to move them downstream when they are ready to leave the system.  SYRCL, CSPA, and other conservation organizations, as well as staff from fisheries agencies, have recommended such a change in release pattern during the ongoing relicensing of YCWA’s hydropower project.

Some of this water released in the summer of 2020 was also sold out of the watershed, generally to entities south of the Delta.  In the fiscal year ending June 30, 2021, YCWA also made $12 million on water sales.2 The large flow increase at the end of August 2020 – likely a water sale – had no benefit for fish.  Its biggest effect on fish was that It drew down storage in New Bullards Bar Reservoir, which created a cascading effect in the very dry year 2021, when flows for all purposes were limited by lack of stored water.

2021

In a very dry year like 2021 that follows a dry year like 2020, river flows in spring and summer (Figure 3) become a major limiting factor.  First, there are no late-winter, early-spring flow pulses to attract adult spring-run salmon.  At a flow of 400 cfs at the bottom end of the lower Yuba River, there is insufficient flow to help adult spring-run salmon move upstream through many shallow riffles and through the Daguerre ladders.  Very low late-summer and fall low flows likewise hinder fall-run salmon.  Second, flows in late winter and early spring are too low to efficiently carry juvenile salmon downstream while avoiding the many predators on their way to the Bay and ocean.  Downstream of Daguerre Dam, over-summering juvenile salmon and steelhead must contend with low flows and associated stressful water temperatures.  Additionally, spawning at 400 cfs flow leads to redd scour if fall rainstorms occur: a late-October storm in 2021 brought Yuba flows up to 15,000 cfs and raised water levels nearly 10 feet (Figure 4).

Habitat

Feeding and cover habitat in the lower Yuba River are virtually nonexistent.  Predatory fish abound below Daguerre Dam.  Floodplain off-channel habitat and woody debris are severely lacking, especially during when winter-spring river flows are relatively low.  Many fall-run salmon spawn in poor spawning habitat below Daguerre.  To its credit, YCWA has contributed on a voluntary basis to several habitat improvement projects in the lower Yuba River, including the ongoing restoration at Hallwood.  However, it has vigorously resisted the establishment of regulatory requirements for additional projects.

Biological Opinion (BO)

Keeping the ladders clean is already a mandate.

  • Measures shall be taken by the Corps to minimize the effects of debris maintenance and removal at the Daguerre Point Dam fish ladders.
  • When Yuba River flows exceed 4,200 cfs, the Corps shall provide notifications to NMFS on the status of debris accumulations and fish passage conditions at the Daguerre Point Dam fish ladders.
  • The Corps shall take action within 24 hours, or as soon as it is safe, to remediate fish passage conditions related to debris maintenance and removal at the Daguerre Point Dam fish ladders.
  • The Corps shall, by January 31 of each year, report to NMFS an update on previous year’s debris maintenance and removal actions, including details on amount of debris removed, the timing of removal and the conditions that triggered debris accumulation.
  • The Corps should consider predator removal at Daguerre Point Dam.

 Summary and Conclusions

Flow regimes and habitat improvements are necessary to save Yuba salmon, in addition to ladder repairs and cleaning at Daguerre Dam.  The Yuba River Accord, which has defined lower Yuba River flows since 2008, leaves too much flow in the summer by shorting flows that salmon and steelhead need in the spring.  The channel of the lower Yuba River also needs extensive physical improvement.

Figure 1. Yuba River salmon escapement 1953-2020.

Figure 2: Yuba River flow (cfs) March 1 – September 15, 2020 above (orange) and below (blue)
Daguerre Dam.

Figure 3. Yuba River flow (cfs) March 15 – September 15, 2021 above (orange) and below (blue) Daguerre Dam.

Figure 4. River flow (cfs) and stage (feet) in lower Yuba River below Daguerre Dam near Marysville in fall 2021.

  1. See YCWA financial report for 2021 and 2020 at https://www.yubawater.org/Archive.aspx?ADID=310, pdf p. 14.
  2. Id. Compare wet year 2019, with likely no out of basin water sales, and water sale revenues of $531 thousand.

Another Threat to Winter-Run Salmon in 2021 – Fall Sacramento River Bypass Overflows

Record late-October Valley rainfall brought Sacramento River flows high enough to overflow into the Tisdale Bypass (Figures 1 and 2).  Such early-fall overflows are highly unusual (Figure 3). The sudden surge filled nearly 30 square miles of the Sutter Bypass before exiting to the south, back to the Sacramento River (Figure 4).  Bypass channels rose 6-10 feet during the storm, with the help of tributary inflows (CDEC gage data not shown), flooding much of the agricultural fields, levee borrow pits, duck club ponds, and natural wetlands and ponds of the Sutter Bypass.

Riding the wave of river flow were juvenile winter-run salmon moving down the Sacramento River (Figure 5).  Many spilled over the weir into the Bypass and into flooded habitats.

After the storms, a sudden drop in flow quickly drained the Sutter Bypass, and many juvenile salmon became stranded in ponds and fields of the Bypass floodplain.  The problem with the short-lived early fall flooding is that stranded habitats dry up or become too warm too sustain the young salmon through the fall, winter, or even spring (if the Bypass does not flood again).  Predation by abundant non-native predatory fish in the Bypass is another problem, especially as the high flows of muddy water retreat.

Also at issue is the attraction of upstream migrant adult fall run-salmon into the Bypass.  Such salmon get trapped downstream of the Tisdale Weir.  The Tisdale Weir Rehabilitation and Fish Passage Project is supposed to mitigate this situation.  But it is only in the planning and design stages, and until that project is complete, adult salmon will continue to be trapped below Tisdale Weir.  In addition, the Tisdale Weir project “does not analyze the impacts to additional special status fish (juvenile salmonids) being attracted into bypass from extended days of inundation and subsequently being stranded without adequate drainage or a plan to mitigate for that.” (Project EIR).  The Tisdale Weir project also needs to plan for and mitigate the juvenile stranding in the Sutter Bypass.

Until the Tisdale Weir Project addresses these issues, fall spills into the Sutter Bypass from flood control weirs on the Sacramento River will reduce survival of winter-run salmon and other anadromous salmonids of the Sacramento River and its tributaries.

Figure 1. The Tisdale Weir and Bypass from the Sacramento River to the Sutter flood bypass.

Figure 2. Overflow (cfs) into the Tisdale Bypass from the Sacramento River 10/24-26/2021. Data Source: CDEC.

Figure 3. Tisdale Weir overflows 1998-2019.

Figure 4. Sutter Bypass properties subject to flooding from Tisdale Weir overflow.

Figure 5. Juvenile salmon collection in screw traps in Sacramento River near Tisdale Weir Aug-Nov 2021.