Monthly Archives: December 2016

Suisun Bay Marsh Habitat

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Wet years have led to high production of salmon, steelhead, smelt, sturgeon, splittail, shad, and striped bass in the Central Valley and Bay-Delta. One of main reasons for this high production is that Suisun Bay and Marsh habitat come into play in winter and spring when freshwater dominates the area under high Delta outflows.

High flows from winter-spring storms carry the young of these species from rivers and the Delta into the Bay. Longfin and Delta smelt even spawn in the Bay and adjacent Napa River. In my own personal experience1 surveying the area in winter-spring of the wet years 1978 and 2006, I observed very high use by young of these species, indicating the area’s high importance as a rearing area for estuarine and anadromous fishes. My experience mirrors that of 35 years of study in the Marsh by Peter Moyle at UC Davis.2

Even in dry years, moderate winter Delta outflow from infrequent winter storms pushes freshwater and young anadromous and estuarine fishes into Suisun Bay/Marsh. Rearing in the Bay and Marsh favors survival of juvenile fish for many reasons, chief among them shallow turbid freshwater that provides abundant food, cool waters through spring, and protection from predators. Fish in the Bay and Marsh also have greatly reduced risk of being lost in the interior Delta to poor habitat, abundant predators, the export pumps, and other water diversions.

Once young fish get to the Bay, they grow quickly and become gradually more tolerant of brackish waters that return after the storms. Salmon, steelhead, longfin smelt, and sturgeon make a full transition and move to the lower Bay and ocean. The Delta smelt, splittail, and striped bass remain in the brackish water through the summer and fall, taking advantage of abundant food and the cooler waters of the Bay. No other region offers these advantages and necessary habitat conditions to the anadromous and estuarine fish species of the Central Valley and Bay-Delta.

Efforts have been ongoing for several decades to restore habitat in Suisun Bay-Marsh. Most recently, the restoration has come under the wing of the State Resources Agency’s EcoRestore program with several new projects, most notably the Tule Red project along the north shore of Grizzly Bay (Figure 1). Other potential sites include Wheeler Island, Chipps Island, and Winter Island, in part by including existing duck hunting clubs under active management. These three sites should be actively pursued by EcoRestore, because they could be restored to tidal marsh. Under existing conditions, their low levees are often overtopped during high winter tides in storm surges, allowing young salmon to enter. However, these fish become trapped when water levels drop. Opening these habitats to the tide would provide new habitat and eliminate stranding.

Figure 2 shows a flooded Wheeler Island. The Collinsville area offers many restoration options including Montezuma Island, the old Navy base, and the old PG&E power plant site. Managed wetland areas adjacent to Montezuma Slough within the Marsh offer many opportunities for tidal habitats along the slough (Figure 3). Among all the above opportunities, only Tule Red is included in EcoRestore (Figure 4). EcoRestore should take greater advantage of the existing high value of Suisun Bay-Marsh habitats and the high potential benefits per unit cost of projects in this area compared to other planned projects upstream in the Delta and Valley.

Returning to where this article started, fish need the winter and spring flows to get them to Suisun Bay-Marsh and to sustain them. Even the driest years have winter storms that partly accomplish this despite the capture of most dry year the rain and snowmelt in Valley reservoirs. Thus, dry year storm pulses become so essential. The state and federal water projects in the Delta also covet these storm pulses and divert significant parts of them through the Delta pumps. The proposed Twin Tunnels would take even bigger bites out of dry year storm pulses3 before they are “lost” to the Bay and ocean. Instead, storm pulses should be enhanced in drier years by allowing a reasonable amount of Valley reservoir inflows to pass through the reservoirs and by limiting diversions of storm pulses from the Delta.

Figure 1. Recommended restoration sites in Suisun Bay. CSPA owns 14 acres along the shoreline near Collinsville below the number 6. (Basemap Source: Suisun Marsh Plan)

Figure 1. Recommended restoration sites in Suisun Bay. CSPA owns 14 acres along the shoreline near Collinsville below the number 6. (Basemap Source: Suisun Marsh Plan)

Figure 2. Flooded Wheeler Island on north shore of Honker Bay. Island levees breached in 2005 and have been marginally repaired. Without active management such sites may become permanently breached and actively eroded. See Figure 1 for location. (Source: GoogleEarth)

Figure 2. Flooded Wheeler Island on north shore of Honker Bay. Island levees breached in 2005 and have been marginally repaired. Without active management such sites may become permanently breached and actively eroded. See Figure 1 for location. (Source: GoogleEarth)

Figure 3. Habitat map of Suisun Bay/Marsh. (Source: Suisun Marsh Plan)

Figure 3. Habitat map of Suisun Bay/Marsh. (Source: Suisun Marsh Plan)

Figure 4. EcoRestore projects. (Source: http://resources.ca.gov/ecorestore/ )

Figure 4. EcoRestore projects. (Source: http://resources.ca.gov/ecorestore/ )

 

  1. Cannon, T. and T. Kennedy, 2007. Fish Use of Shallow Water Habitats of the Western Delta 1978-79 and 2002-07, May 2007. ↩
  2. https://californiawaterblog.com/2011/07/28/the-future-of-suisun-marsh/ ↩
  3. The Tunnel proposal does recognize the importance of the storm pulses for the Bay and would allow some of the first pulse to pass. ↩

Obsession with Fall X2

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There is a science-management obsession with Fall X2 – the location of the 2 parts-per-thousand salinity location in the Bay-Delta in the autumn.  More specifically, Fall X2 is the average km location of X2 for the months of September-December.  Such an average index seems ridiculous given that X2 varies so much especially in December, or even in a year like 2016 in October-November.  Despite this, resource agencies have been intent on trying to manage the Delta smelt population by manipulating Fall X2 based on the relationship between Fall X2 and the following spring 20-mm survey smelt index shown in Figure 1.  Fall X2 is an element of Action 4 in the Smelt OCAP Biological Opinion.

Figure 1. Fall X2 versus 20-mm Survey Delta smelt index.

Figure 1. Fall X2 versus 20-mm Survey Delta smelt index.

The problem is not that fall flows and X2 location are not important to Delta smelt. It’s that the previous year’s winter-through-fall flows, Delta exports, and fall adult population abundance are all related to the subsequent year’s production of smelt. So are winter-spring conditions. Smelt production in any year is related to all these factors, with some factors being more important in some years. A spring index can be low for many reasons, including bad conditions that spring regardless of the location of X2 the previous fall.

Focusing on any one parameter like Fall X2 is dangerous. Since there is only limited water in a drought year, it is critical that available water be distributed in a way it does the most good. If all the smelt die in June, it doesn’t help much to allocate a lot of water in the fall.

Figure 2. River kilometer reference locations for X2. Collinsville (km 81), Mallard Island, and Port Chicago are standard reference locations when specifying X2 standards.

Figure 2. River kilometer reference locations for X2. Collinsville (km 81), Mallard Island, and Port Chicago are standard reference locations when specifying X2 standards.

The Fall X2 factor is being studied in the FLaSH program.1 The study is being undertaken as an adaptive management experiment. “According to the FLaSH conceptual model, conditions are supposed to be favorable for Delta Smelt when fall X2 is approximately 74 km or less, unfavorable when X2 is approximately 85 km or greater, and intermediate in between (Reclamation 2011, 2012). Surface area for the LSZ at X2s of 74 km and 85 km were predicted to be 4000 and 9000 hectares, respectively (Reclamation 2011, 2012).”

The Smelt BO is being revised by the US Fish and Wildlife Service. The State Board is considering new Delta water quality standards for the Delta. Let’s hope they place less emphasis on the Fall X2 factor and more emphasis on progressively managing hydrology, water quality, and fish populations in the Bay-Delta.

Winter-Run Salmon Emigration and First Fall-Winter Rains

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In a recent post I discussed the importance of the first fall rains in stimulating the emigration of juvenile winter-run Chinook salmon from the Redding/RedBluff spawning and rearing area of the Sacramento River below Shasta Dam.

Juvenile salmon trap and seine data from fall and early winter of 2015 and 2016 further support the importance of these first-of-season rains to the emigration of winter-run salmon emigration to the Delta, Bay, and ocean. The pertinent data were obtained from trap and seine collections from four locations (Red Bluff, Tisdale-Wilkins, Knights Landing, and Sacramento) shown in Figure 1.

This year’s (2016) fall migration pattern (Figure 2) shows the marked uptick in movement (catch) with the late October storms. Movement had begun gradually in early September from Red Bluff to Tisdale Weir, with some fish showing up at Sacramento. Most of the fish located above Sacramento seemed to take advantage of the storm-water surge, since the plots for the cumulative capture of juvenile salmon at the Red Bluff, Tisdale Weir, and Knights Landing locations flattened off after the storms.

The previous year’s (2015) migration pattern (Figure 3) indicates that the fish waited until the first storms at the end of fall and beginning of winter before moving from the river into the Delta at Sacramento. The March movements indicated in Sacramento and Chipps Island (entrance to SF Bay) trawl catches are indicative of February-March stocking of hatchery smolts near Redding – these larger smolts are not readily detected in river screw traps and seines.

A recent study report1 describes how low flows result in “long in-river residence and low survival whereas strong peak flows corresponded to rapid emigration and high survival… Overall, this study highlights the importance of pulsed flow conditions for promoting higher survival of juvenile Winter-Run Chinook Salmon emigrating to the ocean.” The study notes that survival is proportional to the cumulative catch. Note that the catch in 2016 is nearly 50% higher so far than it was in 2015.

The recent data confirms the need to bypass some of the inflow to Central Valley rim dams during early storm pulses. This bypass of flow to spawning and rearing areas just downstream of the dams gets salmon moving downstream. It is equally important to limit Delta exports during these peak juvenile emigration periods. Success during storm events is critical for endangered salmon to reach the Bay and ocean.

Figure 1. Location of four trap and seine locations in Sacramento River between Red Bluff (river mile 243) and Sacramento (river-mile 54).

Figure 1. Location of four trap and seine locations in Sacramento River between Red Bluff (river mile 243) and Sacramento (river-mile 54).

Figure 2. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall 2016 plus river flow at Wilkins Slough gage (CDEC data).

Figure 2. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall 2016 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data).

Figure 3. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall-winter 2015 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data)

Figure 3. Winter-run Chinook salmon cumulative catch at Sacramento River collection sites in fall-winter 2015 (www.cbr.washington.edu/sacramento), plus river flow at Wilkins Slough gage (CDEC data)

  1. http://scienceconf2016.deltacouncil.ca.gov/sites/default/files/2016-11-02-Accepted-Poster-Abstracts.pdf. Emigration Rate and Survival of Winter-run Chinook Salmon. Jason Hassrick, ICF International, jason.hassrick@icfi.com. Arnold Ammann, NOAA Southwest Fisheries Science Center, arnold.ammann@noaa.gov. p. 64. ↩