California Code of Regulations › Title 23 - Waters › Division 6 - Delta Stewardship Council › Chapter 2 - Consistency with Regulatory Policies Contained in the Delta Plan › Article 4 - GENERAL PROVISIONS › Appendix 3 - Habitat Restoration*

Current through Register 2024 Notice Reg. No. 28, July 12, 2024
[FN*]
The Council adopts this document as part of section
					 5006. It therefore has regulatory
					 effect despite the markings on the document indicating it is a 'draft'.
II. Habitats
ERPP Goal 4 (Habitats) is to protect and/or restore
					 functional habitat types in the Bay-Delta estuary and its watershed for
					 ecological and public values such as supporting species and biotic communities,
					 ecological processes, recreation, scientific research, and aesthetics. The ERPP
					 identified a number of key habitat types for which conservation and restoration
					 would be pursued in the Delta. These habitat types are continuing to be
					 reviewed and evaluated as a part of various habitat conservation plans in terms
					 of the natural communities they seek to conserve, and within the ERP. As these
					 evaluations are completed, scientists and managers will have a better
					 understanding of these natural communities, and will be better able to monitor
					 status and trends in these natural communities at a regional scale, as well as
					 build this information into future management plans.
There were two strategies in the Delta Vision Strategic
					 Plan associated with the creation and restoration of habitat: Strategy 3.1,
					 "Restore large areas of interconnected habitats--on the order of 100,000
					 acres--within the Delta and its watershed by 2100"; and Strategy 3.2,
					 "Establish migratory corridors for fish, birds, and other animals along
					 selected Delta river channels". These two strategies describe actions regarding
					 inundation of floodplain areas, restoration of tidal and riparian habitat, and
					 protection of grasslands and farmlands.
Development of the Delta Conservation
					 Strategy Map.
This element in the Conservation Strategy
					 contributes to identification of restoration opportunities within the Delta,
					 primarily based on land elevations with consideration of current urban land use
					 constraints (Figure 4). Existing non-urban land uses, infrastructure, and other
					 constraints at these locations were not considered for this map. These features
					 will be addressed in future analyses of site-specific proposals. Figure 4
					 presents existing elevations in the Delta, which we consider a starting point
					 for developing priorities for habitat restoration. Several broad habitat types
					 were identified for restoration and have been classified according to three
					 ranges of land elevation: upland areas, intertidal areas, and subsided
					 lands/deep open water areas. Appendix E provides a crosswalk between habitat
					 categories in this Conservation Strategy for the Delta and those in the ERP
					 Plan.
In accordance with the recommendations in the Delta Vision
					 Strategic Plan and in light of expected sea level rise, the areas of the Delta
					 that are of highest priority for restoration include lands that are in the
					 existing intertidal range, floodplain areas that can be seasonally inundated,
					 and transitional and upland habitats. Assuming a rise in sea level of
					 approximately 55 inches over the next 50-100 years (Cayan et al. 2009), these
					 areas would become shallow subtidal, seasonaly inundated floodplain, and
					 intertidal and upland habitats respectively. The next highest priority for
					 restoration to tidal marsh would be lands below the intertidal range that are
					 not highly subsided, and are within the range of feasibility for subsidence
					 reversal projects. The lower elevation boundary of subsided lands appropriate
					 for tidal marsh restoration has not been established, and may vary depending on
					 location, configuration, availability of dredge spoils, and other factors that
					 may promote or inhibit soil accretion associated with vegetation establishment.
					 The most subsided lands would be the lowest priority for restoration to tidal
					 marsh because raising elevations to the range appropriate for vegetation
					 establishment is likely to be in feasible. However, these deeply subsided lands
					 may have value as deep water habitat, although the benefits of increasing deep
					 water habitat in the delta ecosystem have not been established.
Click
					 here to view image
Figure 4: Land elevations in the Delta and Suisun Marsh.
					 Current land elevations will largely determine what habitat types can be
					 accomodated.
Delta Agricultural Lands.
It
					 is important to note that a significant portion of the land within the Delta is
					 dedicated to agricultural production, some of which is considered suitable for
					 habitat restoration. Despite this, it is projected that much of this land will
					 remain dedicated to agriculture into the future. Expected reductions in the
					 availability of freshwater for all beneficial uses, due to changing
					 precipitation patterns and extended droughts, means that sea level rise will
					 increase salinity in some areas of the Delta, particularly the western and
					 central Delta, even absent any natural perturbations such as an
					 earthquake-induced levee breach of a major Delta island. There simply will not
					 be enough freshwater in the future to continue maintaining all parts of th
					 freshwater pool year-round. It is therefore probable that Delta agriculture
					 will adapt naturally over time to these expected changes in the Delta, through
					 a combination of planting more drought- and salt-tolerant crops as agricultural
					 biotechnology becomes more widely available; growing crops that can be used to
					 produce ethanol or other biofuels; seeking more opportunities for
					 cultural/economic diversification (e.g., ecotourism); and managing for wetlands
					 and associated plants for wildlife benefits rather than agriculture and/or
					 toward development of a carbon emissions offset trading market. Some U.S.
					 Department of Agriculture programs already exist that provide financial
					 incentives for landowners to manage natural areas on their properties,
					 including but not limited to the Wildlife Habitat Incentives Program, the
					 Environmental Quality Incentives Program, and the Conservation Reserve Program.
					 While largely successful in other States, funding for implementation of these
					 programs in California must be augmented to make participation more attractive
					 to landowners who face higher capital and production costs. ERP will continue
					 to fund projects on agricultural lands which benefit wildlife and help ensure
					 that agricultural properties are conserved.
ERPP Vision for Agricultural Lands:
Improve
					 associated wildlife habitat values to support special-status wildlife
					 populations and other wildlife dependent on the Bay-Delta. Protecting and
					 enhancing agricultural lands for wildlife would focus on encouraging production
					 of crop types that provide high wildlife habitat value, agricultural land and
					 water management practices that increase wildlife habitat value, and
					 discouraging development of ecologically important agricultural lands for urban
					 or industrial uses in the Sacramento-San Joaquin Delta and Suisun Marsh/North
					 San Francisco Bay Ecological Management Zones.
ERPP volume 1, July 2000
ERPP Vision for Tidal Perennial Aquatic
					 Habitats
: Increase the area and improve the quality of existing
					 connecting waters associated with tidal emergent wetlands and their supporting
					 ecosystem processes. Achieving this vision will assist in the recovery of
					 special-status fish, wildlife, and plant populations and provide high-quality
					 aquatic habitat for other fish, wildlife, and plant communities dependent on
					 the Bay-Delta. Restoring tidal perennial aquatic habitat would also result in
					 higher water quality and increase the amount of shallow-water and mudflat
					 habitats; foraging and resting habitats and escape cover for water birds; and
					 rearing and foraging habitats, and escape cover for fish.
ERPP volume 1, July 2000
Delta Upland Areas.
Connectivity of existing habitat to higher elevation areas will be critical for
					 Delta habitats and species with rising sea level, global warming, and regional
					 climate change. As the sea level rises, existing intertidal habitat will become
					 subtidal, and adjacent uplands will become intertidal. Additionally, adjacent
					 higher elevation habitat will be critical for wildlife to escape flooding.
					 Changes in regional climate are expected to result in precipitation patterns of
					 more rain and less snow, shifting tributary peak runoff from spring to winter,
					 making extreme winter runoff events more frequent and intense, and bringing
					 about longer dry periods in summer. In light of these expected changes, and
					 ongoing conversion of open space lands to urban uses, some of these higher
					 elevation areas will be expected to accommodate additional flood flows in new
					 or expanded floodplain areas.
Upland areas in the Delta are best characterized as lands
					 well above current sea level (i.e., greater than five feet in elevation,
					 depending on location). Aquatic habitats in this category include
					 seasonally-inundated floodplain, seasonal wetlands (including vernal pools),
					 and ponds, while terrestrial habitats in this category include riparian areas,
					 perennial grasslands, and inland dune scrub, as well as agricultural lands.
					 Protecting and creating a mosaic of different upland habitat types that are
					 well distributed, and connected to other natural communities is important for
					 maintaining genetic diversity of the numerous species which use these areas for
					 all or part of the life cycles. The aquatic and terrestrial habitat types that
					 comprise upland areas often co-occur (e.g., agricultural lands that are
					 seasonally inundated to benefit waterfowl, and perennial grasslands that
					 support vernal pools). Thus, this habitat category highlights the importance of
					 preserving and enhancing a diversity of habitats in support of numerous species
					 and ecological processes, as well as allowing the system to respond to drivers
					 of change such as sea level rise.
Stage 2 Actions for Upland Areas:
Action 1:
Acquire land and easement interests
					 from willing sellers in the East and South Delta that will accommodate seasonal
					 floodplain areas, and shifts in tidal and shallow subtidal habitats due to
					 future sea level rise.
Action 2:
Conduct research to determine scale
					 and balance of flow, sediment, and organic material inputs needed to restore
					 riverine ecosystem function.
Action 3:
Develop a better understanding of
					 species-habitat interactions, species-species interactions, and species
					 responses to variable ecosystem conditions in order to better determine natural
					 versus human-induced responses of upland habitat restoration.
Action 4:
Determine contaminant and runoff
					 impacts of agriculture and urban areas, and develop predictions of effects on
					 the ecosystem from future expansion of these land uses.
Action 5:
Restore large-scale riparian
					 vegetation along waterways wherever feasible, including opportunities for
					 setback levees.
The rationales for protection and enhancement of seasonal
					 wetlands, vernal pools, riparian areas, perennial grasslands, and inland dune
					 scrub are contained in the ERP and the reader is encouraged to refer to these
					 volumes for more information (CALFED 2000b). For the purposes of this
					 Conservation Strategy, the discussion on restoring upland habitats will be
					 focused on seasonally-inundated floodplains and protection of agricultural and
					 open space lands for wildlife-compatible uses.
With increasing sea level, global warming, and regional
					 climate change, uplands adjacent to Delta tidal fresh and brackish wetlands
					 will be important for future uphill colonization of these wetlands. In light of
					 these expected changes, protection of uplands from ongoing conversion to urban
					 uses should be a high priority to allow adaptation to climate change and
					 maintain sustainable natural aquatic communities into the future.
Much has been learned since 2000 about creating habitats in
					 upland areas, particularly with respect to seasonally-inundated floodplains and
					 their importance to many of the Delta's aquatic species. As knowledge has
					 increased, the risk and uncertainty associated with restoring this habitat is
					 decreasing. Thus, restoration of seasonally-inundated floodplains is a very
					 high priority for the Delta in the near term.
Delta Floodplain.
A natural
					 floodplain is an important component of rivers and estuaries that allows many
					 essential ecological functions to occur. Healthy floodplains are
					 morphologically complex. They include backwaters, wetlands, sloughs, and
					 distributaries that carry and store floodwater. Floodplain areas can constitute
					 islands of biodiversity within semi-arid landscapes, especially during dry
					 seasons and extended droughts. The term
floodplain
as used
					 here means the generally flat area adjoining rivers and sloughs that are
					 inundated every 1.5 to 2 years when flows exceed the capacity of the channel
					 (bank full discharge). Peak flows in winter and spring that occur every 1.5 to
					 2 years are considered by river geomorphologists to be the "dominant discharge"
					 that contributes the most to defining the shape and size of the channel and
					 distribution of sediment, bar, and bed materials. Larger flood events can cause
					 major changes to occur, but they do not happen often enough to be the decisive
					 factor in river geomorphology.
Floodplain areas have the potential to support highly
					 productive habitats, as they represent a heterogeneous mosaic of habitats
					 including riparian habitat, freshwater tidal marsh, seasonal wetlands,
					 perennial aquatic, and perennial grassland habitats, in addition to
					 agricultural lands. During inundation floodplains are used by numerous native
					 fish for spawning and early growth (Moyle 2002). There has been extensive
					 research on the Yolo Bypass and lower Cosumnes River, in addition to some
					 research the Sutter Bypass, indicating that native resident and migratory fish
					 show a positive physiological response (i.e., enhanced growth and fitness) when
					 they have access floodplain habitats (Moyle et al. 2004, Ribeiro et al. 2004,
					 Moyle et al. 2007), which likely benefits them as they complete subsequent
					 stages of their respective life cycles. Inundated floodplain areas provide
					 important spawning and rearing habitat for splittail and rearing habitat for
					 juvenile Chinook salmon (Sommer et al. 2001, Sommer et al. 2002, Moyle et al.
					 2007). Splittail need about 30 consecutive days of floodplain inundation to
					 produce good survival through the larval stage and survival improves with
					 longer durations (Moyle et al. 2004). Without access to adequate floodplain
					 spawning habitat, splittail reproduction declines drastically as seen during
					 the late 1980s and early-1990s.
Managing the frequency and duration of floodplain
					 inundation during the winter and spring, followed by complete drainage by the
					 end of the flooding season, could favor native fish over non-natives (Moyle et
					 al. 2007, Grimaldo et al. 2004) and reduce nuisance insect problems. Frequency,
					 timing, and duration of inundation are important factors that influence
					 ecological benefits of floodplains. To favor splittail recruitment and benefit
					 salmon fry and smolt growth, DFG recommends during above normal and wet years,
					 once 10 days of floodplain inundation have been achieved based on runoff and
					 discharge from upstream reservoirs between January 1 and May 30, then reservoir
					 discharges should be continued to maintain uninterrupted inundation for at
					 least 30 days in the Yolo Bypass and at suitable locations in the Sacramento
					 River or the San Joaquin River (DFG 2010b).
Studies on the Cosumnes and Sacramento Rivers indicate that
					 dynamic processes are needed to support complex dynamic riparian habitats and
					 upland systems which form the floodplain habitat (Moyle et al. 2007). Native
					 plants and animals have adapted to the random brief floodplain events that are
					 characteristic of California's hydrology. Riparian habitats would be a
					 component of these future restoration actions. Extant riparian habitats exist
					 along levees and at the higher elevations in intertidal habitats, and in
					 floodplain habitats -- usually on fluvial soils or where levees are created
					 with a mineral soil. The voluntary recruitment of this habitat type on Prospect
					 Island and the higher elevation areas of Liberty Island and Little Holland
					 Tract underscore the proclivity of natural restoration when proper soil
					 conditions and elevation occur.
Stage 2 Actions for Floodplains:
Action 1:
Continue coordination with Yolo
					 Basin Foundation and other local groups to identify, study, and implement
					 projects on public or private land with willing participants, to create
					 regionally significant improvements in habitat and fish passage.
Action 2:
Continue implementing projects at
					 the Cosumnes River Preserve, such as restoring active and regular flooding
					 regimes and flood riparian forest habitat; measuring flora and fauna response
					 to restoration; and monitoring surface and groundwater hydrology and geomorphic
					 changes in restored areas.
Action 3:
Pursue opportunities for land and
					 easement acquisitions in the Yolo Bypass and along the lower Cosumnes and San
					 Joaquin Rivers, which could be utilized as floodplain inundation areas in the
					 near term or in the future.
Research on the Cosumnes River also shows the many
					 ecosystem benefits that floodplains provide. The Cosumnes River is the only
					 remaining unregulated river on the western slope of the Sierra Nevada. The
					 Cosumnes River Preserve comprises 46,000 acres. The free-flowing nature of the
					 river allows frequent and regular winter and spring overbank flooding that
					 fosters the growth of native vegetation and the wildlife dependent on those
					 habitats. In addition to the value of floodplain habitat to the Delta's native
					 species, floodplains are believed to enhance the estuarine food web, as they
					 support high levels of primary and secondary productivity by increasing
					 residence time and nutrient inputs into the Delta (Sommer et al. 2004). Ahearn
					 et al. (2006) found that floodplains that are wetted and dried in pulses can
					 act as a productivity pump for the lower estuary. With this type of management,
					 the floodplain exports large amounts of Chlorophyll
a
to the
					 river. Floodplain habitat on the Cosumnes River Preserve has been shown to
					 provide many benefits to native fish (Swenson et al. 2003, Ribeiro et al. 2004,
					 Grosholz and Gallo 2006, Moyle et al. 2007).
Because floodplain areas are inundated only seasonally,
					 many other habitat types that occur in upland areas can be accommodated on
					 floodplains when high winter and early spring flows are not present. The
					 Department of Water Resources Flood Protection Corridor Program provides grant
					 funding to local agencies and nonprofit organizations for nonstructural flood
					 management projects that include wildlife habitat enhancement and/or
					 agricultural land preservation, and acquisition of flood easements. Such
					 easements provide a way to bring floodplain benefits to species seasonally,
					 while also accommodating agricultural production in summer, fall, and early
					 winter. Delta crops such as rice, grains, corn, and alfalfa provide food for
					 waterfowl and other terrestrial species, and, with appropriately timed plowing
					 and harvest, may serve as surrogate habitat in the absence of historical
					 habitat such as tidal marsh. From Highway 99 west to the Cosumnes River
					 Preserve is a good example of an area that provides a wildlife-friendly
					 agriculture mix. It is the largest conservation easement acquisition funded by
					 ERP during Stage 1. The ERP also provided funding for planning activities or
					 property acquisitions and restoration of wildlife friendly agriculture in the
					 Yolo Bypass, along the Cosumnes River, and along the San Joaquin River near
					 Mossdale Crossing.
Although the benefits of floodplains have been
					 demonstrated, there are several cautions related to restoring seasonal
					 floodplains:
* Restoration must incorporate as much natural connection
					 with the river as possible to reduce potential stranding of native fish.
					 Large-scale flooding events also help reduce stranding by creating channels on
					 the landscape which allow for natural drainage, and multiple pulse flows help
					 ensure fish receive the migratory cues they need. Deep drainage canals or other
					 unnatural scour holes deeper than a couple feet should be removed. Such areas
					 remain too cool during drainage and don't provide the emigration cues needed
					 for most fishes.
* The periodic wetting and drying of floodplain areas make
					 these areas especially prone to methylmercury production and transport. Within
					 the context of the Delta Total Maximum Daily Load (TMDL) for methylmercury that
					 is currently being developed, floodplain restoration activities should include
					 the investigation and implementation of Best Management Practices (BMPs) to
					 control methylmercury production and/or transport.
Delta-Upland Transitional
					 Corridor.
The establishment of a corridor of protected
					 agricultural and natural lands is needed to protect valuable habitats and to
					 facilitate movement of wildlife between the the Delta's Cache Slough area and
					 the Denverto Slough in Suisun Marsh, this area currently contains a mosaic of
					 perennial grassland and vernal pool areas, and has been identified by local
					 planners as having great potential for ecological benefits from
					 restoration.
Dune Scrub Habitat.
Two ERP
					 grants have been used to fund surveys to locate potential habitat restoration
					 sites capable of supporting Antioch dunes evening primrose, Contra Costa
					 wallflower, and Lange's metalmark butterfly. Potential areas were located and
					 are being assessed for enhancement, but no enhancement has been funded nor have
					 funds for annual monitoring and reporting been identified. Continuing
					 evaluation and enhancement of dune scrub habitat is needed during Stage 2
					 implementation.
Delta and Suisun Marsh Intertidal
					 Areas.
Tidal marshes across North America have been shown to
					 play a critical role for native fish by providing improved foraging
					 opportunities, increased growth, and refuge from predators (Boesch and Turner
					 1984, Baltz et al. 1993, Kneib 1997, Madon et al. 2001). The tidal marshes of
					 the Delta have received relatively little study; however, research conducted in
					 the San Francisco Estuary and elsewhere along the Pacific coast has shown tidal
					 marsh benefits to native fish, especially salmonids (Simenstad 1982, West and
					 Zedler 2000, Bottom et al. 2005, Maier and Simenstad 2009).
Intertidal areas in the Delta are best characterized as
					 lands between one and seven feet above sea level, depending on location (Figure
					 4). All lands in the intertidal range are assumed to have the ability to
					 support some tidal marsh habitats (either brackish or freshwater) with
					 associated mudflats, sloughs, channels, and other open water features. Some
					 areas are capable of supporting large areas of contiguous habitat, and others
					 may support only small patches (e.g., mid-channel islands and shoals). Properly
					 functioning tidal marsh habitats have subtidal open water channels with systems
					 of dendritic and progressively lower-order intertidal channels that dissect the
					 marsh plain. These diverse habitats provide structure and processes that
					 benefit both aquatic and terrestrial species.
The rationales for protection and enhancement of fresh and
					 brackish tidal marsh areas are contained in the ERPP, and the reader is
					 encouraged to refer to these volumes for more information (CALFED 2000a). For
					 the purposes of this Conservation Strategy, the discussion on restoring
					 habitats in intertidal areas will focus on what has been learned about the
					 importance of these areas since 2000, particularly as it relates to various
					 species' use of tidal marsh areas and the role of these areas in enhancing the
					 aquatic food web.
ERPP Vision for Saline Emergent Wetland:
Increase the area and protect the quality of existing saline emergent wetlands
					 from degradation or loss. Wetland habitat will be increased to assist in the
					 recovery of special-status plant, fish, and wildlife populations. Restoration
					 will provide high-quality habitat for other fish and wildlife dependent on the
					 Bay-Delta.
ERPP Vision for Fresh Emergent Wetland:
Increase the area and improve the quality of existing fresh emergent wetlands
					 from degradation or loss and increase wetland habitat. Achieving this vision
					 will assist in the recovery of special-status plant, fish, and wildlife
					 populations, and provide high-quality habitat for other fish and wildlife
					 dependent on the Bay-Delta.
ERPP volume 1, July 2000
Studies of species' use of tidal marsh habitat in the Delta
					 are limited, but ERP and other programs have conducted several studies since
					 the ROD that continue to augment knowledge regarding the role of intertidal
					 habitats for desirable aquatic species. The largest effort to study tidal marsh
					 habitat in the Delta and its benefits to native fish was a series of projects
					 known as the BREACH studies (Simenstad et al 2000), which investigated
					 geomorphology, sedimentation, and vegetation at four reference sites and six
					 restored tidal marsh sites in the Delta. Of the one reference and three
					 restored sites sampled for fish and invertebrates, relative density of both
					 native and introduced fish species was higher at the reference marsh (Simenstad
					 et al. 2000). Although all of the sites were dominated by the introduced fish,
					 the abundance of native fish was highest in winter and spring (Grimaldo et al.
					 2004). In stomach content analyses, all life stages of chironomids (midges)
					 were shown to be a very important food source for fish, both adjacent to tidal
					 marsh habitats and in open water areas. Chironomid association with marsh
					 vegetation indicates the importance of this habitat to the aquatic food
					 web.
Overall abundance of fish larvae was highest in marsh edge
					 habitat when compared to shallow open water and river channels (Grimaldo et al.
					 2004). Unfortunately, the BREACH study sites are not representative of the
					 Delta's large historical marshes. Most sites are small and severely degraded
					 areas located along the edge of levees or on small channel islands.
An example of an ongoing study of species use of tidal
					 marsh within intertidal land elevations is the ongoing monitoring associated
					 with restoration of Liberty Island, a 5,209-acre island in the northern Delta
					 that breached naturally nearly ten years ago. The Liberty Island project
					 provides a good example of passive restoration of various habitat types,
					 including some deeper, open water, subtidal and freshwater emergent tidal marsh
					 and sloughs with riparian habitat at the higher elevations at the northern end.
					 Liberty Island's sloughs are populated with otters, beavers, muskrats, and
					 numerous species of ducks and geese. Native fish species using the area include
					 Chinook salmon, splittail, Longfin and delta smelt, tule perch, Sacramento pike
					 minnow, and starry flounder. In some areas, native species account for up to 21
					 percent of the fish collected; for reference, native species only account of
					 approximately 2 to 10 percent elsewhere (Malamud-Roam et al. 2004). Ongoing
					 monitoring at Liberty Island for almost eight years is showing that fish
					 species assemblages at this restored area increasingly resemble assemblages at
					 reference marsh sites. The ERP hopes to build upon the success of this
					 restoration project by increasing the size of the project and developing a
					 dendritic channel system on its interior (DFG 2008b).
In many estuaries of the Pacific Northwest, including the
					 Columbia and Fraser river estuaries, Chinook salmon fry usually occupy shallow,
					 near shore habitats including tidal marsh, where they feed and grow and adapt
					 to salt water (Healey 1982; Levy and Northcote 1982; Simenstad et al. 1982).
					 They often move far up into tidal wetlands on high tides, and may return to the
					 same channels on several tidal cycles (Levy and Northcote 1982). In estuaries
					 throughout Washington, subyearlings and fry occur mainly in marshes when these
					 habitats are available (Simenstad et al. 1982). Tidal marsh restoration has
					 been shown to result in recovery of life history diversity in the Salmon River
					 estuary of Oregon. Tidal marsh habitat in this estuary had largely been lost
					 due to diking by the early 1960s (Gray et al. 2002). In surveys conducted in
					 the mid-1970s, Chinook salmon juveniles were found to rear in the estuary only
					 to a limited extent during the spring and early summer months (Bottom et al.
					 2005b). Three sites in the estuary were restored to tidal action between 1978
					 and 1996 and by the early 2000s juvenile salmon were making extensive use of
					 restored marsh habitats for rearing, with estuarine resident times up to
					 several months (Bottom et al. 2005b). Tidal marsh restoration expanded life
					 history variation in the salmon population; the amount of time spent rearing in
					 the estuary was variable and juveniles moved into the ocean over a broad range
					 of time and at a broad range of sizes (Bottom et al. 2005b). Chinook salmon
					 show remarkable phenotypic plasticity in their ability to adapt to new
					 locations and form multiple life history types from a single introduction of
					 fish (Williams 2006); with restoration of tidal marsh in the Delta, Chinook
					 salmon in the Sacramento and San Joaquin rivers may be able to regain varied
					 life history types over time.
A number of additional studies are demonstrating that
					 regardless of species actual use of marsh areas, these habitats could be
					 extremely important for their possible role in augmenting the Delta's aquatic
					 food web, particularly in the saline portion of the estuary.
* Tagging and stomach content studies show that Chinook
					 salmon fry may use intertidal habitat. According to Williams (2006), tagged
					 hatchery fry remain in the Delta up to 64 days and tend to occupy shallow
					 habitats, including tidal marsh. Stomach contents of salmon rearing in the
					 Delta are dominated by chironomids and amphipods, suggesting that juvenile
					 salmon are associated with marsh food production. Juvenile salmon in the Delta
					 also undergo substantial growth (Kjelson et al. 1982, Williams 2006). These
					 findings coincide with studies elsewhere in the Pacific Northwest (Healey 1982,
					 Levy and Northcote 1982, Simenstad et al. 1982),which found that Chinook salmon
					 fry usually occupy shallow, near-shore habitats including tidal marshes,
					 creeks, and flats, where they feed and grow and adapt to salt water (Healey
					 1982; Levy and Northcote 1982; Simenstad et al. 1982), and that they often move
					 into tidal wetlands on high tides and return to the same channels on several
					 tidal cycles (Levy and Northcote 1982). Also, in estuaries throughout
					 Washington, subyearlings and fry occur mainly in marshes when these habitats
					 are available (Simenstad et al. 1982). In fact, Healey (1982) identified
					 freshwater tidal marshes as the most important habitat to juvenile salmon in
					 the Pacific Northwest. More recently, in the Columbia River estuary, emergent
					 tidal marsh has been shown to support the greatest abundance of insects and
					 highest stomach fullness scores for juvenile salmon, with chironomids again
					 being the dominant prey type (Lott 2004).
* In a study of carbon types and bioavailability, tidal
					 marsh sloughs in Suisun Bay had the highest levels of dissolved, particulate,
					 and phytoplankton-derived carbon (Sobczak et al. 2002). Chlorophyll
a
concentration, used as a measure of standing crop of
					 phytoplankton, was highest in tidal sloughs and supports the greatest
					 zooplankton growth rate (Mueller-Solger et al. 2002) when compared to other
					 habitat types, such as floodplains and river channels. High levels of primary
					 production (as measured by Chlorophyll
a
) seen in several
					 regions in the interior of Suisun Marsh are likely due to high residence time
					 of water, nutrient availability, and absence of non-native clams (DFG
					 2008b).
* Modeling (Jassby et al. 1993 and Cloern 2007) and
					 empirical studies (Lopez 2006) show that productivity from high-producing
					 areas, such as marsh sloughs, is exported to other connected habitats.
					 Phytoplankton biomass location is only weakly correlated with phytoplankton
					 growth rates across several aquatic habitats. Therefore other processes,
					 including mixing and transport, are important in determining phytoplankton
					 distribution in the Delta. The data shows that Suisun Marsh plays a significant
					 role in estuarine productivity by providing an abundant source of primary
					 production and pelagic invertebrates, both of which are significantly depleted
					 in bay and river channel areas (DFG 2008b).
Tidal marsh may also help improve the pelagic food web by
					 reducing the concentration of ammonium in the water. Ammonium has been shown to
					 inhibit phytoplankton blooms in Suisun Bay and possibly other open-water
					 habitats in the Delta by inhibiting the uptake of nitrate by diatoms (Wilkerson
					 et al. 2006, Dugdale et al. 2007). In a nutrient-rich estuary in Belgium, tidal
					 freshwater marsh was shown to transform or retain up 40 percent of ammonium
					 entering the marsh during a single flood tide (Gribsholt et al. 2005).
					 Nitrification (the conversion of ammonium to nitrate) accounted for a large
					 portion of the transformation (30 percent). Nitrification rate in the marsh
					 system was measured at 4 to 9 times that which occurs in the adjacent water
					 column (Gribsholt et al. 2005). Increased tidal marsh habitat may, therefore,
					 improve the base of the aquatic food web in the Delta by increasing primary
					 production within the marshes, and by increasing the ratio of nitrate to
					 ammonia in the estuary.
At the outset of ERP, restoration of intertidal and shallow
					 subtidal areas (at that time termed "shallow water habitat", defined as water
					 less than two meters in depth at mean lower low water) was a very high
					 priority, and based on what has been learned since 2000, continues to be a very
					 high priority for the Delta. However, the extensive spread of non-native
					 submerged aquatic vegetation (SAV) in intertidal and shallow subtidal areas
					 renders them less suitable for native fish (Nobriga et al. 2005, Brown and
					 Michniuk 2007, Nobriga and Feyrer 2007). Brown and Michniuk (2007) reported a
					 long-term decline in native fish abundance relative to non-native fish. This
					 decline in native fish abundance occurred coincident with the range expansion
					 of non-native SAV (principally
Egeria densa
) and non-native
					 black bass (centrarchids), both of which are discussed further in the Stressors
					 section below. Predation by largemouth bass is one mechanism hypothesized to
					 result in low native fish abundance where SAV cover is high (Brown 2003,
					 Nobriga et al. 2005). Largemouth bass have a higher per-capita predatory
					 influence than all other piscivores in SAV-dominated intertidal zones (Nobriga
					 and Feyrer 2007). Restoration of Delta intertidal habitats must, therefore, be
					 designed and managed to discourage non-native SAV, or native fish may not
					 benefit from them (Grimaldo et al. 2004, Nobriga and Feyrer 2007).
In summary, restoration of tidal marsh areas in the Delta
					 remains a very high priority for the ERP; however, several cautions must be
					 kept in mind. A major concern is that restored tidal marsh would be colonized
					 by non-native species, which would in turn limit the benefits to native
					 species. Another potential constraint facing the restoration of intertidal
					 habitats is the methylation of mercury in sediments. Therefore, restoration of
					 tidal marsh within intertidal land elevations should be designed as large-scale
					 experiments, and should be rigorously monitored to establish relationships
					 between this habitat and species population abundance. As this information
					 continues to be collected and synthesized, the risk and uncertainty associated
					 with restoring this habitat are expected to decrease.
Subsided Delta Lands and Deep Open Water
					 Areas.
Subsided land areas in the Delta are best characterized
					 as land well below current sea level (below approximately six feet in
					 elevation), and include both terrestrial areas (islands that have subsided over
					 time) and deep open water areas (subsided islands that flooded in the past and
					 were never reclaimed). Aquatic habitats in this category include seasonal
					 wetlands and ponds that occur within subsided land areas, in addition to deep
					 open water areas that occur on flooded islands such as Franks Tract and Mildred
					 Island (also called pelagic habitat).
With increasing sea level, global warming, and regional
					 climate change, the existing configuration of Delta levees and deeply subsided
					 islands are not expected to remain intact over the long term. A forecast rise
					 in sea level of approximately 55 inches over the next 50-100 years (Cayan et
					 al. 2009) is expected to increase pressure on the Delta's levee system. Changes
					 in regional climate and the shift of tributary peak runoff from spring to
					 winter are expected to make extreme winter runoff events more frequent and
					 intense, further compounding pressure on Delta levees seasonally. In light of
					 these expected changes, in addition to human-induced impacts (e.g., increased
					 runoff from continued conversion of open space land to urban uses), there is a
					 considerably higher likelihood of Delta levee failure and subsequent island
					 flooding in the future. ERP implementation must therefore adapt to these
					 expected pressures, including planning for optimizing the value of newly-flood
					 deep islands for the aquatic species that may utilize them in the
					 future.
Stage 2 Actions for Subsided Lands/Deep Open Water
					 Areas:
Action 1:
Implement wildlife-friendly
					 agriculture and wetland projects.
Action 2:
Secure easements and land on which
					 subsidence reversal projects can occur.
Action 3:
Continue research on the creation
					 and management of deep open water areas (e.g., Liberty Island) to evaluate
					 physical and biological properties and species use.
Terrestrial areas in this category include mainly
					 agricultural lands, some of which are not in active agricultural production.
					 Central Valley Joint Venture (2006) recognizes that agricultural easements to
					 maintain waterfowl food supplies and buffer existing wetlands from urban
					 development may become increasingly important in basins where large increases
					 in human populations are predicted. In addition, ongoing rice cultivation may
					 help minimize subsidence. Subsidence reversal, carbon sequestration, and
					 wildlife-friendly agricultural projects are appropriate on these deep islands
					 in the near term, as they are expected to provide benefits to the local
					 economy, wildlife, and waterfowl while protecting lands from uses that may be
					 unsustainable over the longer term.
The rationales for protection and enhancement of seasonal
					 wetlands and wildlife-friendly agriculture are contained in the ERPP, and the
					 reader is encouraged to refer to these volumes for more information (CALFED
					 2000b). For the purposes of this document, the discussion on restoring habitats
					 on subsided lands will be focused on subsidence reversal and carbon
					 sequestration, and on continuing to research and restore deep open water areas
					 for the Delta's pelagic fish species, as these deep open water habitat types
					 are known to be important, positively or negatively, for individual pelagic
					 fish species.
Delta Subsidence Reversal.
The exposure of the bare peat soils to air causes oxidation and decomposition,
					 which results in subsidence, or a loss of soil elevation, on Delta islands.
					 Flooding these lands and managing them as wetlands reduces their exposure to
					 oxygen, so there is less decomposition of organic matter, which stabilizes land
					 elevations. Wetland vegetation cycles lead to biomass accumulation, which
					 sequesters carbon and helps stop and reverse subsidence (Fujii 2007). As
					 subsidence is reversed, land elevations increase and accommodation space (the
					 space in the Delta that lies below sea level and is filled with neither
					 sediment nor water), on individual islands is reduced (Mount and Twiss 2005). A
					 reduction in accommodation space decreases the potential for drinking water
					 quality impacts from salinity intrusion in the case of one or more levee breaks
					 on deeply subsided Delta islands.
A pilot study on Twitchell Island funded by the ERP in the
					 late 1990s investigated methods for minimizing or reversing subsidence. The
					 study showed that by flooding soils on subsided islands approximately one foot
					 deep, peat soil decomposition is stopped, and conditions are ideal for emergent
					 marsh vegetation to become established. In the Twitchell Island pilot project,
					 researchers saw some initial soil accumulation during the late 1990s and early
					 2000s, and noted that accretion rates accelerated and land surface elevation
					 began increasing much more rapidly after about seven years, as plant biomass
					 was accumulated over time. Land surface elevation is estimated to be increasing
					 at an annual rate of around four inches, and is expected to continue to
					 increase (Fujii 2007).
The USGS is interested in implementing a subsidence
					 reversal program Delta-wide, given the results of their Twitchell Island pilot
					 study. Such a program would involve offering financial incentives to landowners
					 to create and manage wetland areas on their lands (Fujii 2007). Large-scale,
					 whole-island approaches to reversing subsidence would be beneficial for
					 multiple purposes. Programs that offer incentives for 10- or 20-year studies
					 for subsidence reversal on large tracts of land could help improve Delta levee
					 stability and reduce the risk of catastrophic failure. Assuming that accretion
					 rates continue at about four inches annually, estimates suggest a 50 percent
					 reduction in accommodation space in 50 years if subsidence could be pursued
					 throughout the Delta. This reduction in accommodation space jumps to 99 percent
					 over the next 100 years (Fujii 2007). Some deeply subsided lands could also be
					 used as disposal sites for clean dredged sediments, providing local flood
					 control improvements while helping raise land elevations on subsided islands
					 more quickly. This accommodation space reduction, in addition to helping
					 stabilize levees over the longer term, would create additional areas for
					 restoration of additional tidal marsh habitat.
While the primary objectives of creating wetlands on deep
					 Delta islands would be to reverse subsidence and sequester carbon, there would
					 be significant ancillary benefits to wildlife such as waterfowl. Delta
					 agricultural lands and managed wetland areas provide a vital component to
					 Pacific Flyway habitat for migratory waterfowl by increasing the availability
					 of natural forage, ensuring improved body condition and breeding success
					 (CALFED 2000b).
Deep Open Water Habitat.
All
					 permanent aquatic habitats in the Delta are occupied by fish of some type. In
					 planning for restoration of Delta aquatic habitats, it is important to consider
					 which fish will occupy which habitat and when; and what type of benefits fish
					 will gain from the habitat. Fish assemblages in the Delta, each with a distinct
					 set of environmental requirements, include native pelagic species (e.g., delta
					 and longfin smelt), freshwater planktivores, dominated by non-native species
					 such as threadfin shad and inland silverside; anadromous species (e.g., salmon
					 and steelhead), slough-residents associated with beds of SAV (e.g.,
					 centrarchide), and freshwater benthic species (e.g., prickly sculpin) (Moyle
					 and Bennett 2008). Habitat diversity is necessary to support multiple fish
					 assemblages in the Delta. Restoration efforts need to focus on creating
					 habitats required by desirable species, while avoiding habitats dominated by
					 undesirable species.
With the increasing threats of levee failure from
					 continuing land subsidence, exacerbated by sea level rise, higher seasonal
					 runoff, and random events such as an earthquake, the Delta is likely to have
					 more large areas of deep, open water in the future (Moyle and Bennett 2008).
					 Important attributes to manage to increase habitat variability and provide
					 improved water quality conditions include salinity, contaminant inputs, and
					 connectivity to surrounding habitats (Moyle and Bennett 2008). Fish assemblages
					 will respond differently to future environmental changes.
New open water habitats may also result from intentional
					 activities on a smaller and more managed scale than whole-island flooding. The
					 intentional removal of levees on islands at the periphery of the Delta in order
					 to create marsh habitat on elevations would result in open water below the
					 tidal zone similar to that which is developing at Liberty Island. Exchange of
					 materials between the restored tidal marsh and adjacent open water could result
					 in higher productivity in open water habitat. As mentioned in the discussion on
					 tidal marsh restoration, the potential for SAV dominated by non-native species
					 to establish in new shallow water environments is a concern. On Liberty Island,
					 SAV has not become a dominant component of the open water habitat. This may be
					 a result of tidal flow velocities, wind-induced disturbance and high
					 turbidities, or some other factor. Continuing research and monitoring of the
					 Liberty Island project will improve understanding of the dynamics of a large
					 island breach at the periphery of the Delta, and help plan for future marsh or
					 open water restoration projects.
There are many uncertainties related to future
					 characteristics of flooded island and open water habitats (Moyle and Bennett
					 2008). These include configuration and location of flooded islands; physical
					 properties such as depth, turbidity, flow, and salinity; biological properties
					 such as productivity of phytoplankton and copepods; and susceptibility to
					 invasion by non-native species such as
Egeria densa
,
					 centrarchids, and invasive nonnative clams. Adaptive management, combined with
					 large-scale experimentation on new open water habitat, would help to reduce
					 uncertainties. This could occur through the planned flooding of at least one
					 Delta island, or through an organized study plan that would go into effect in
					 the event of an unplanned levee breach (Moyle and Bennett
					 2008).
1. New
					 appendix filed 8-7-2013; operative 9-1-2013 pursuant to Government Code section
					 11343.4(b)(3)
					 (Register 2013, No. 32).