A New Paradigm for Sacramento River Basin Salmon Habitat Restoration

Posted on June 11, 2015 by Dave Vogel

Nearly everyone supports the concept of restoring salmon and their habitats within the existing geographic range of the Central Valley. But why is it so difficult to implement relatively low-cost, simple actions that would unquestionably benefit salmon? The following is a recent example of the problem and its ultimate, surprising solution.

In 1986, a colleague (Dick Painter) with the Department of Fish and Game [now Department of Fish and Wildlife (DFW)], through a lot of planning and hard work, created an excellent salmon habitat project in a side channel on the main stem Sacramento River in Redding, California. Many years later, I named this area “Painter’s Riffle” in recognition of the dedicated biologist. The modified channel worked well for many years but, inevitably, the habitat quality diminished due to lack of fresh gravel replenishment that would have been historically provided from upstream areas prior to construction of Shasta and Keswick dams. Nevertheless, the area proved beneficial for 25 years by being hydraulically connected to the main river and provided habitats for the river’s four runs of salmon and steelhead. This circumstance changed dramatically after the City of Redding widened the Highway 44/299 Bridge spanning the Sacramento River just upstream of Painter’s Riffle. As is now usual and customary for such in-river projects, DFW required the bridge contractor to lay clean spawning gravels in the riverbed (amounting to 20,000 cubic yards) as a platform to commence work. The concept being, after the bridge project was complete, high reservoir releases from Shasta Dam would eventually wash those gravels downstream and contribute to new salmon spawning areas. The strategy worked … somewhat. The gravel mobilized en masse during March of 2011 when Shasta Reservoir went into flood-control releases and 50,000 cubic feet per second surged into the river below Keswick Dam. The gravels placed under the highway project flushed downstream, but left 8,000 cubic yards in the channel’s entrance, forever plugging Painter’s Riffle.

In early February 2013, while driving across the new Highway 44/299 Bridge, I looked downstream and could readily see what had happened — Painter’s Riffle had been hydraulically disconnected from the river. I drove to the site (a City of Redding municipal park) to take some photographs and measurements. That night, I wrote a Proposal to restore the site to its original ecological function and presented the concept to the City of Redding, obtaining its support. However, when I met with DFW representatives (including a “Habitat Restoration Coordinator”) to garner the agency’s support, you would have thought I’d wacked a hornet’s nest! My read on the less-than-enthusiastic response was that any “outsider” involvement and alternative scientific perspectives in their internal plans for salmon restoration were unwelcomed. This was revealed months after my original Painter’s Riffle proposal when a radically different proposal for the site surfaced and was sanctioned by the fish agencies. They recommended slicing a 10-foot wide trench through the same side channel and only allowing it to function at flows above 10,000 cfs, instead of my submittal which recommended the channel perform at 3,250 cfs, or the minimum reservoir releases. In my written response to the agencies’ proposal, I explained that winter-run Chinook salmon redds would become stranded and eggs would perish in the side channel if the fish spawned during normal flows above 10,000 cfs (among many other problems). After many months of valuable time lost, logical minds prevailed and the agencies’ proposal was quietly removed from consideration.

To gain momentum, the project needed an advocate and was proposed to the Golden Gate Salmon Association’s (GGSA Interview) Task Force which includes the three fish agencies: DFW, USFWS, & the National Marine Fisheries Service (NMFS). DFW & NMFS representatives were contemplatively silent, but a USFWS representative asserted he had already looked at the site and the gravels appeared to be too large for suitable salmon spawning (paradoxically, in direct conflict with DFW’s in-river project gravel requirements). The effort was rapidly dying on the vine and, without badly-needed support, GGSA was forced to put the proposal on the back burner.

Trying a different venue, the project was presented to northern California water districts. Surprisingly, the Glenn-Colusa Irrigation District (GCID), located nearly 100 river miles downstream of Painter’s Riffle said they would champion the cause (aka, do the on-the-ground work). At this point, with the winds shifting once again in the salmon’s favor, GGSA went to the U.S. Bureau of Reclamation (USBR) and requested their staff to take the task on as part of GGSA’s Salmon Plan. They were successful. Although it was still 2013, the reality of the extensive regulatory permitting hurdles forced USBR staff to eventually concede that it would be impossible to implement the project until the following year, even though low river flows (Shasta Reservoir releases) due to the severe drought would have provided perfect conditions for construction. Regrettably, the salmon would have to wait until the fall of 2014.

As anticipated from long-range weather forecasts, the heavy rains never arrived during the winter of 2013-2014, but the meetings, conference calls, and draft environmental documents on the proposed Painter’s Riffle project came on like a deluge. The scales were now tipping against restoration. In fact, except for GCID, USBR, and GGSA, it seemed no fish entity would formally support the project. For example, the USFWS suggested “pre-project monitoring” be conducted at the sealed-off side channel before any gravel was moved, perhaps for many years. Undefined “concerns” were voiced about effects on threatened and endangered fish, but without remedial recommendations and recognition of the benefits. With this much resistance, it seemed as though we were proposing to build a new waste-water treatment plant on the river that would spew raw sewage into the middle of prime salmon habitats. The quagmires of state and federal bureaucracies were sucking the enthusiasm for the restoration effort down into the black hole of oblivion. Nevertheless, after numerous speed bumps in the process and a seemingly endless series of meetings and conference calls, the log jam broke and key pragmatic agency individuals came on board with the project.

Now, at this late date, with renewed zeal, a Herculean effort was set in motion by USBR and GCID staff who worked overtime to update and finalize the numerous regulatory permits to implement the project in the fall of 2014. But wait, not so fast! This simple project almost came to a screeching halt when Endangered Species Act restrictions nearly imposed insurmountable obstacles to conduct the in-river work. At the 11^th hour, several knowledgeable, rational DFW biologists stepped up to the plate and delivered on all fronts with support, cooperation, and assistance resulting in NMFS allowing the work to proceed.

Once NMFS gave its blessing, the field implementation to restore Painter’s Riffle went into overdrive because of advanced planning and the due diligence of highly experienced GCID heavy equipment operators. Two massive front-end loaders, a D-6 cat bulldozer, and an excavator simultaneously went into close-quarter action. Their execution was well choreographed with all four earth-moving machines weaving up and down and across Painter’s Riffle. Each operator knew the movements of others through radio communication, hand signals, or most often, years of experience in skilled operation of the machines. It was mesmerizing to watch the quick transformation of the river channel: Video of Equipment in Action

With everything going smoothly and swiftly, Mother Nature had another plan. One of the largest storms to hit northern California in years (ironically, in a fourth-consecutive drought year) slammed into the area during the two weeks of construction. With heavy rains and winds pummeling the equipment crew, they relentlessly proceeded nonstop during permitted hours. And, to be sure, this was no ordinary storm. The so-called “Atmospheric River” or “Pineapple Express” parked itself on top of Redding for an extended period and localized flooding was reported everywhere. Caltrans even made an emergency stop at the job site to clear plugged culverts spewing heavy rain runoff in the municipal park. Although Shasta Reservoir was extremely low due to the three prior years of drought, the downstream re-regulating Keswick Dam suddenly had to increase water releases due to localized flooding concerns in the vicinity of the dam. River flows at the construction site increased dramatically, jeopardizing the work in progress … but the crew diligently kept on working and completed the project ahead of schedule and below budget.

Ultimately, all involved agencies, groups, and individuals praised the project and the unprecedented collaboration. The finished product is anticipated to benefit the Sacramento River’s four runs of Chinook salmon and steelhead. As a result, new salmon restoration projects are planned for implementation this and next year … using more-active stakeholder involvement and “outsiders” perspectives. Perhaps there is hope for salmon after all: Video of Completed Project

The completed Painter’s Riffle Project.

Drought Effect on the Bay

Posted on June 9, 2015 by Tom Cannon

During the past four years of drought little has been said about the specific effect of the drought on the Bay, especially the upper Bay. Suisun Bay is a very important part of the San Francisco Bay Estuary as it receives freshwater flow from the Delta and is the low salinity mixing zone of the Bay-Delta ecosystem. Suisun Bay is also critical habitat of many listed estuarine and anadromous fishes. The drought has brought something new: unprecedented high salinities to Suisun Bay from relaxed Bay-Delta Plan Delta outflow and salinity standards. In the chart below (Figure 1) salinity levels as measured by micro-mhos of electrical conductivity (EC) were high (>15,000 EC) at Port Chicago in west Suisun Bay in April and May 2014 and 2015. Normal dry year levels are shown by 2012, when the Delta Outflow standard is 7100 cfs and the Collinsville salinity standard is 2780 EC. In 2014 and 2015, the standards were relaxed to save reservoir storage. The Outflow standard was reduced to 4000 cfs. The salinity standard location was moved upstream into the Delta. Although unregulated flow dominated most of the Apr-May period in 2012 (Figure 2), the regular standards applied in the latter half of May.

Figure 1. Salinity (EC) in Suisun Bay in April-May 2012, 2014, and 2015.

The potential ramifications of these unprecedented low outflows and high salinities are wide ranging and substantial.

Invasive species will increase their presence in the Bay-Delta. Clams, zooplankton, and fish communities will change. Invasive Potamocorbula clams abundance has likely increased and moved further upstream¹. More clams mean less plankton and higher selenium concentrations in clams.

“The biomass of the larger copepods is less than it was before the introduction of the clam Corbula amurensis, because of competition for food and grazing by clams on the early life stages of copepods. The resulting low abundance of copepods of suitable size, and the long food chain supporting them, may be contributing factors to the decline in abundance of several estuarine fish species.”²

“Many scientists in the U.S. geological survey, who have been studying the Bay for decades, also concur with Strong, that the clam is likely the culprit”.³
Young Longfin and Delta Smelt have been forced to rear in the Delta rather than the Suisun Bay. Mysid and Bay shrimp production will be lower.
Concentration of contaminants will be higher in Suisun Bay, possibly leading to toxicity to plankton, benthic invertebrates, and fish.
Unbalanced levels of ammonia, nitrogen, and phosphorous nutrients will lead to trophic changes in the plankton community (e.g. more blue green algae and lower diatom production).
Less inflow to Suisun Bay means less organic carbon and other nutrients necessary to stimulate the estuary’s food chain. Turbidity from river sediment will be lower.

Less inflow to the Delta and less outflow to the Bay also mean more nutrients, plankton, and fish are drawn to the South Delta export pumps. Even with restricted pumping at 1500 cfs limit, the effect is proportional and significant. In reality, Delta outflows are lower than the NDOI estimates provided by DWR and Reclamation. A 14-day running average relaxed standard of 4000 cfs often leads to “real” outflows closer to zero⁴.

More on the effects of outflow on Suisun Bay can be found at:
http://www.sfestuary.org/wp-content/uploads/2015/03/Estuary-MAR2015-v8a-finalWEB.pdf .

Figure 2. Delta outflow (NDOI) in April-May 2012, 2014, and 2015.

Record Heat in the Delta: A Challenge to Reclamation

Posted on June 7, 2015 by Tom Cannon

Despite a relatively cool May, the Delta is very warm under conditions of low river and Delta flows and low outflow to the Bay that the State Water Board has allowed by weakening flow standards. As in 2014, water temperatures in early June approach the lethal level for Delta Smelt of 73°F¹ (Figure 1). The water temperatures now (and in 2014) are several degrees higher than in 2012, the last year in which the normal dry year flow standards were followed.

The first heat wave of summer, with air temperatures forecasted from 95-100°F, is predicted to begin early next week. Water temperatures in the entire Delta are expected to reach the lethal level of 73°F or higher. The water temperature may be further degraded in the north and central Delta by the opening of the Delta Cross Channel in combination with the new False River Barrier (FAL location on map).

Delta Smelt are presently confined primarily to the Sacramento Deep Water Ship Channel, where water temperatures are already near lethal levels (Figures 2 and 3). Reclamation scientists theorize that smelt can survive in deeper, cooler waters. I challenge Reclamation to prove this theory by monitoring water temperature and taking dissolved oxygen profiles throughout the Sacramento Deep Water Ship Channel all summer.

Figure 1. Water temperature in the Delta in first week of June 2015.
Based on water temperatures recorded at CDEC stations (blue dots).

Figure 2. Water temperature in the Sacramento Deep Water Ship Channel,
May 28 – June 6, 2015.

Figure 3. Distribution of Delta Smelt catch in 20-mm Smelt Survey May 2015.
All but three young smelt were captured in the Sacramento Deep Water Ship
Channel . Water temperature at the time of the net deployment in the
Channel was 65°F (at surface).

Incipient lethal temperatures for Delta Smelt in laboratory conditions are 75-77°F. In the wild, Delta Smelt are virtually never found in water whose temperature is greater than 73°F. ↩

Bay-Delta Fisheries Devastated by Weakened Protections

Posted on May 26, 2015 by Tom Cannon

Water quality standards under the jurisdiction of the State Water Resources Control Board provide bare minimal protections to the State’s major ecosystems in Critically Dry years. But with the extended drought in seven of the past nine years, protections have been weakened to the point where ecosystems and fisheries dependent on them have been devastated. Yes, rice acreage is down 25%¹, but fish production is down 95%, with some species lost forever. Salmon numbers have been maintained by hatcheries and trucking hatchery production to the Bay, but not without a huge mortgage on future wild populations. Hatchery salmon already make up over 90% of ocean and river fisheries. Delta Smelt, Longfin Smelt, Steelhead, Green and White sturgeon, Striped Bass, and wild Chinook Salmon populations have declined another 90% in the past four years, after losing 90% in each in the past several decades. Farm production will return, but some fish will not. The ecosystem will return, but with a much different makeup of new food web plankton species from Asia, greater proportions of non-native sport and pan fish, and a greater assortment of the invasive aquatic plants that already fill waterways. The Delta will be featured more often on the Bass Masters Classic.

And what about the Bay? Only a few hundred thousand acre-feet of water of the millions released from reservoirs this summer will reach the Bay. Water quality and marine fish and shellfish will soon show signs of decline. The Bay-Delta is a major nursery for anchovies, herring, and Dungeness crab. Anchovy stocks are already collapsing². Sea lions are starving and dying.

How hard would it be to at least maintain the antiquated minimum protections adopted in 1995 Bay-Delta Standards? The Bay is “allocated” a base of about 5 million acre-feet of water each year in the form of a base Delta outflow of 7,100 cfs. This standard for critically dry years is the first to suffer from State Board drought orders. The Board has reduced outflows requirements to 3000-4000 cfs (Figure 1). Such low outflows are in reality closer to zero (see earlier blog³). The amount of water “short” from the critical year base in the important February – June period is approximately 300,000 acre-feet. This amounts to less than 5% of the total 10 million acre-feet of reservoir releases into the Central Valley in 2014 and expected in 2015. The amount is less than 10% of the 5 million acre-feet presently in storage in Central Valley reservoirs. The water could be restored to the Bay by reducing water contractor allocations and/or reservoir storage.

The Delta had one plankton bloom that came and went this spring⁴. Plankton blooms are needed to drive the Bay-Delta food chain. Without freshwater flow to the Bay there will be no blooms and little food through the summer for Bay-Delta fishes. Water quality will suffer as well. The prognosis for the Bay-Delta and other California ecosystems is grim. California fisheries will suffer for decades to come.

Figure 1. Delta outflow as calculated by the California Department of Water Resources for Feb-May, 2015. Top red line represents 7100 cfs minimum standard. Lower red line represents typical weakened level of protection.

Sacramento Bee reports tomato production reached 14 million tons last year, a record. Milk production revenue jumped 24 percent in 2014. http://www.sacbee.com/news/state/california/water-and-drought/article21958428.html ↩
http://www.montereyherald.com/opinion/20150502/db-pleschner-west-coast-sardine-decline-science-vs-politics ↩
http://calsport.org/fisheriesblog/?p=87 ↩
http://calsport.org/fisheriesblog/?p=219 ↩

Early May Prognosis for Smelt

Posted on May 18, 2015 by Tom Cannon

How are Delta and Longfin smelt doing after my earlier March and April poor prognoses? As predicted, late April – early May surveys indicated extremely low numbers (Figures 1 and 2), far fewer than the record low numbers of 2013-2014 (Figures 3-6).

In the May 4, 2015 Smelt Working Group meeting¹, “Members did make a note of the single Delta Smelt larva from April 23, as well as the three Delta Smelt observed during the primary channel CO2 treatment [at Tracy Fish Salvage Facilities], providing that this is evidence of entrainment. These collections occurred despite at or below minimum exports levels, as defined in the Biological Opinion; OMR flows were also at or close to the most positive flows indicated in the Biological Opinion….Salvage of juvenile Longfin Smelt increased to 52 for the week of April 27 through May 3. Some increase was expected as south Delta water warmed. Between April 13 and 15, four juvenile Longfin Smelt were salvaged at the CVP and 12 at the SWP, at the same time, a single larva was observed in the larval fish samples at the CVP and four larvae at the SWP. During the period of April 17 through 23, seven Longfin Smelt larvae were observed at the SWP and one larva at the CVP in larval fish collections. Continued collections in salvage are expected. Overall, catches in the central and south Delta were not sufficient to reach concern levels based on density or distribution… Longfin Smelt larvae and small juveniles will continue to be detected at the salvage facilities until water temperatures surpass 22 deg C.” The fact that any smelt were collected at the two south Delta export facilities should be a grave warning of a larger and very significant “take” of smelt. As stated many times before, the odds of any young smelt reaching the south Delta export facilities without succumbing along the way are infinitesimal. In addition, no smelt will survive in any part of the Delta where water temperature reaches 25°C.

With the prescribed Net Delta Outflow Index at only 4000 cfs and measured outflow nearer to zero, the low salinity zone critical habitat of smelt is in the central Delta. Remaining smelt are being drawn across the Delta from north to south to the export pumps. Under these conditions the first heat wave of late spring will heat the central Delta to lethal 23-25°C levels for smelt. Unless these conditions are changed by increasing outflow and reducing exports, both smelt species may go virtually extinct² this spring.

Figure 1. Delta Smelt density distribution in late April 20-mm Survey. Only three were captured in Sacramento Deep-Water Ship Channel, compared to 20 in previous week’s survey.