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3 Stressors: Environmental Factors and Their Effects on the Bay-Delta Ecosystem
Pages 57-152

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From page 57...
... In addition, species composition and environmental conditions in the delta have undergone large changes over the period. Therefore, while an immediate difficulty for some is that concern over some listed species has affected water diversions, "the problem" is harder to define biologically, and is perceived differently by various stakeholder groups, institutions, and other interests.
From page 58...
... The Ecosystem and Its Components Do Not Necessarily Respond as a Single Unit to Most Environmental Factors For example, Chinook salmon (Oncorhynchus tshawytscha) spend several years at sea and then return to pass through the delta as adults to spawn; their eggs and young spend time in delta tributaries before passing through the delta on their way to the ocean to mature.
From page 59...
... , these are intimately linked to other biotic components of the ecosystem, including planktonic and benthic primary producers, grazers, larval, and juvenile and mature invertebrate and fish species. SOURCE: Courtesy of A
From page 60...
... , also affect flow patterns, water temperature and quality, food availability, and so on, and they differentially affect many species, even those that do not migrate. There is a complex interplay between key water quality, habitat, and sustainability issues and the drivers affecting them.
From page 61...
... changes in Reservoirs. Impediments and benefits freshwater flow to fish passage.
From page 62...
... Feasibililty of management? Toxic chemicals Inputs of selenium, Concentrations not Selenium: San Joaquin mercury, pesticides.
From page 63...
... Tules have a low salt tolerance, but current water management that keeps the delta fresh for conveyance purposes allows tule wetlands to extend to the margins of Suisun Bay. Their ability to colonize into the subtidal
From page 64...
... and the National Marine Fisheries Service (NMFS) to protect listed fish species, the delta smelt, and Chinook salmon.
From page 65...
... 3 D1641 was finalized in March 2001. 4 Development of Flow Criteria for the Sacramento-San Joaquin Delta Ecosystem, August 3, 2010.
From page 66...
... These four are not independent and are represented in an average sense (to a good degree of approximation) :6 et delta outflow = Sacramento River inflow N + San Joaquin River inflow ­ In-delta diversions Both of the river flows include the effects of reservoir operations (storage and releases)
From page 67...
... The reason is that at steady state the tendency for freshwater flow to carry salt out of the estuary is balanced by the tendency for gravitational circulation and tidal dispersion to carry salt upstream toward the delta. As a result of this balance, the mean position of X2 is proportional to the net delta outflow raised to the minus one-seventh power (Monismith et al.
From page 68...
... When the position of X2 is at 72 km, it requires 1,350 cfs to move X2 1 km downstream, whereas when the position of X2 is at 82 km, it requires 470 cfs to do so. As context, the tidal excursion in Suisun Bay and the western delta is of the order of 10 km.
From page 69...
... However, this conceptual model may be applicable only to conditions existing when X2 is sufficiently far upstream to keep the LSZ in the more channelized sections of the Sacramento and San Joaquin rivers. When the LSZ is in Suisun Bay, energetic horizontal mixing associated with tidal motions over the highly variable bathymetry (Ridderinkhof and Zimmerman 1992, Burau et al.
From page 70...
... 2009) so that, even without any freshwater flow, there would be exchange between the delta and San Francisco Bay.
From page 71...
... (1995) , considering separately the period before 1987 and the period from 1987 to 2006, with 1987 chosen as the approximate start of the Corbula invasion of San Francisco Bay.
From page 72...
... . The panels for striped bass and Pacific herring plot survival indices; all the others show log abundances.
From page 73...
... Thus, while the mechanisms behind the influence of position of X2 on the abundance of a variety of biota remain hypothetical, the statistical relations reported in several papers show that abundance of a number of species at different trophic levels found in the delta and San Francisco Bay is higher when X2 is farther downstream. This implies that sufficient reductions in outflow due to diversions would tend to reduce the abundance of these organisms.
From page 74...
... forms in the LSZ where near-bottom upstream transport by gravitational circulation leads to particle retention (e.g., Geyer 1993) , a mechanism thought for some time to be important in the bay delta (Arthur and Ball 1979)
From page 75...
... more vulnerable to predation. This effect may be more pronounced in the deeper delta channels rather than in the wave-mixed shallows of Suisun Bay.
From page 76...
... (2009) show that, for the San Joaquin system, net flow through the system acts to push the region of maximum temperature downstream toward the ocean.
From page 77...
... In contrast, flow effects that affect San Francisco Bay downstream of the delta, as might be represented in the relations between the position of X2 and abundance, are not amenable to direct engineering intervention in that the only things that can be controlled are timing and volume of flow out of the delta. Given that the position of X2 for different periods of time appears to be important for different species, one can argue that water operations should be designed to preserve as much of both the volume of outflow and the timing of that volume that would be observed in the absence of diversions (Moyle et al.
From page 78...
... High nutrient inputs can lead to altered community structure and proliferation of phytoplankton that may have undesirable effects on biogeochemical cycling, food-web dynamics, habitat conditions, and human health. There are numerous examples of the negative effects of nutrient overenrichment, or "too much of a good thing" (D'Elia 1987)
From page 79...
... However, in some regions of the bay delta where tides are weaker (e.g., the southernmost reach of South San Francisco Bay or the southern interior delta) water residence time may be long enough (especially during low-flow periods)
From page 80...
... pointed out that excessive N loading may also be problematic in South San Francisco Bay, which can have dry weather residence times of several weeks (Gross et al.
From page 81...
... discharged from SWWTP and other anthropogenic sources should be included when considering N input reductions aimed at stemming unwanted symptoms of eutrophication (e.g., cyanobacterial blooms in the upper delta and other nutrient-sensitive regions of the San Francisco Bay, e.g., South San Francisco Bay)
From page 82...
... Food Quality and Quantity: Linking Environmental Stressors to Changes at Base of the Food Web The drastic alteration of the Sacramento­San Joaquin Delta and San Francisco Bay since at least the mid-1800s has led to multiple and interacting physical, chemical, and biological changes (Healy et al.
From page 83...
... . Corbula amurensis, an aggressive invader, has populated the benthic regions of San Francisco Bay and the western delta to the extent where its density has reached 10,000 per m2.
From page 84...
... Conclusions There is a need to distinguish changes in physical drivers such as freshwater discharge, turbidity, temperature, and vertical mixing as well as circulation, from chemical factors, such as nutrient enrichment and changes in nutrient supply ratios, and biological factors, including top-down grazing, as causative agents for changes at the base of the food web and the POD. All of these factors affect rates of primary production, standing stock, and composition of primary producers along the freshwater-to-marine continuum representing the bay-delta system.
From page 85...
... . From 1870 to the early 1900s, other Atlantic species were brought from eastern North America by train and planted in San Francisco Bay; they include oysters, American eels (Anguilla rostrata)
From page 86...
... examined juvenile and adult fishes through the Sacramento­San Joaquin Delta and found that the overall catch was 59 percent nonnative 10"Invasive" species are nonnative species that not only become established but become major components of the ecosystem. 11 This species is designated by some as M
From page 87...
... Despite changes in zooplankton, striped bass survival was not related to the appearance of C amurensis.
From page 88...
... Also, the invasive species can interact with other stressors, which also are affected by other factors than invasives. The linkage between introduced species and fish species of interest is often due to physical alterations of habitat, shifted food base, or changed predation pressure, and we lack the data or models to make these linkages quantitative.
From page 89...
... There are many contaminants, many of which pose risks to different species, in different locations, or at different spatial and temporal scales. Chemical contamination is historically well documented in the San Francisco Bay Delta compared to many coastal environments (e.g., Luoma and Phillips 1988, van Geen and Luoma 1999, Hunt et al.
From page 90...
... . Nevertheless, recent reviews of the pelagic organism decline concluded either that data are insufficient to demonstrate whether contaminants have adverse impacts in nature (Johnson et al.
From page 91...
... ontaminants are too numerous and dispersed, and effects too sporadic and subtle, for any monitoring program to provide useful information for correlative analyses. Thus, these effects must be investigated through more detailed, mechanistic studies." Despite these challenges, San Francisco Bay is also one of only a few estuarine locations where site-specific ecological impacts from contaminants have been clearly shown in the field.
From page 92...
... Using these criteria and the perspective of chemical class, Table 3-2 indicates the highest risks to the bay-delta ecosystem are posed by selenium, mercury, and pesticides. In the 1980s, deaths and deformations in birds, along with the local extirpation of aquatic species, accompanied the disposal of selenium-rich irrigation drainage from the western San Joaquin Valley into the Kesterson National Wildlife Refuge.
From page 93...
... Joaquin Vally. further inputs from Effects on sturgeon Consider San Joaquin the western San and waterfowl in River inputs to bay Joaquin Valley.
From page 94...
... For example, infrastructure changes in the delta such as construction of an isolated facility could result in the export of more Sacramento River water to the south, which would allow more selenium-rich San Joaquin River water to enter the bay. The solutions to selenium contamination must be found within the Central Valley and the risks from selenium to the bay are an important consideration in any infrastructure changes that affect how San Joaquin River water gets to the bay.
From page 95...
... Green sturgeon (Acipenser medirostris) appears to be the species most at risk from chemical contamination.
From page 96...
... Impediments have a range of effects, from slowing the migration by delaying passage, removing fish from the migration corridor to encounter hazardous conditions, or completely blocking access to productive habitat. Dams as Absolute Barriers One prevalent form of passage impediment in the Central Valley is dams that form absolute barriers to migrating fish, in that they have neither ladders for adults nor bypass systems to pass seaward-bound smolts.
From page 97...
... may be even greater, since they had a broader geographic distribution than Chinook salmon. As a result, winter-run and spring-run Chinook salmon, and steelhead populations, are confined to lower-elevation portions of many tributaries as well as the mainstem Sacramento and San Joaquin rivers (NMFS 2009a, b)
From page 98...
... Ultimately this results in reduced population resilience to environmental variation at local and basin-wide scales. The committee concludes that the dams that act as absolute barriers, which have eliminated access to nearly 80 percent of the historical habitat, have been, and continue to be, a major stressor limiting the recovery of ESA-listed anadromous fish species in the Central Valley.
From page 99...
... , thousands of small and medium-size water diversions exist along the Sacramento River, San Joaquin River, and their tributaries. Many remain unscreened.
From page 100...
... 100 TABLE 3-3 Life History Timing for Anadromous Fish Species in the Upper Sacramento River Adult Adult Typical Egg Juvenile Juvenile Species Immigration Holding Spawning Incubation Rearing Emigration Winter-run Chinook Dec ­ Jul Jan ­ May Apr ­ Aug Apr ­ Oct Jul ­ Mar Jul ­ Mar Spring-run Chinook Apr­ Jul May ­ Sept Aug ­ Oct Aug ­ Dec Oct ­ Apr Oct ­ May Fall-run Chinook Jul ­ Dec n/a Oct ­ Dec Oct ­ Mar Dec ­ Jun Dec ­ Jul Late fall-run Chinook Oct ­ Apr n/a Jan ­ Apr Jan ­ Jun Apr ­ Nov Apr ­ Dec Steelhead Chinook Aug ­ Mar Sept ­ Dec Dec ­ Apr Dec ­ Jun Year round Jan ­ Oct Green sturgeon Chinook Feb ­ Jun Jun ­ Nov Mar ­ Jul Apr ­ Jun May ­ Aug May ­ Dec SOURCE: Reproduced from Table 5-1 in NMFS (2009a)
From page 101...
... In contrast, Michel estimated total survival from release in the upper Sacramento River to the mouth of the San Francisco Bay was an order of magnitude lower, ranging from 3.1 to 5.5 percent. Michel also noted that this total survival (which includes the delta segment)
From page 102...
... Recent studies using San Joaquin River fall Chinook salmon smolts estimated survival between 5 and 8 percent as smolts migrated through the south delta, Old River, and reaches leading to the pumps (San Joaquin River Group Authority 2010)
From page 103...
... The available data based largely on Michel's (2010) and the San Joaquin River Group Authority (2010)
From page 104...
... However, actions for San Joaquin fish appear less certain. Should actions divert fish through the tidally dominated central delta or should fish be diverted, collected, and transported at the pumps?
From page 105...
... , and the NRC's previous conclusion on pumping operations (NRC 2010) , we conclude that in some years the population-level impacts on delta smelt are large and thus is a significant factor affecting delta smelt population dynamics.
From page 106...
... Passage impediments at the RBDD and ACID diversion dam contributed to the decline of the ESA-listed anadromous species in the Central Valley. However, improvements in passage at both facilities, ACID in 2001 and RBDD in 2011, appear to have significantly improved passage in the Sacramento River.
From page 107...
... Historical reports indicate the first commercial fisheries in the bay-delta system developed in the mid-1800s and targeted Chinook salmon in the Sacramento and San Joaquin rivers and in Suisun Bay (Scofield 1956, cited in Smith and Kato 1979)
From page 108...
... . Today the bay and delta support recreational fisheries for striped bass, largemouth black bass, white sturgeon, Chinook salmon, steelhead, catfishes (family Ictaluridae)
From page 109...
... 0 1.0 B PROHIBITED STURGEON NDA 0.5 NDA 0 1.0 C STRIPED BASS NDA NDA PROHIBITED 0.5 NDA NDA 0 3 D SHAD 2 PROHIBITED 1 NDA NDA NDA 0 1870 1880 1890 1900 1910 1920 1930 1940 1950 1960 1970 YEAR FIGURE 3-8Commercial fish catches from the San Francisco Bay Delta for (A) Chinook salmon (Sacramento and San Joaquin rivers only)
From page 110...
... Thus, their utility in comparing the importance of exploitation as a stressor among species or among stressors is limited. Further complicating estimation of relative exploitation rates is the fact that many species of interest in the San Francisco Bay-Delta system are diadromous (migrate between saltwater and freshwater)
From page 111...
... for striped bass in the San Francisco Bay-Delta system. R02208 Figure 3-9 bitmapped raster image
From page 112...
... However, we lack definitive evidence that exploitation is a major stressor in the San Francisco Bay-Delta system, especially since the harvest of Chinook salmon and steelhead in California has been tightly controlled recently (green sturgeon, as a listed endangered species, may not be taken)
From page 113...
... The Central Valley spring-run Chinook salmon ESU had as many as 18 or 19 total populations. Today there are three.
From page 114...
... As the percent hatchery contribution on the spawning grounds rise, so will concerns regarding the potential for negative genetic impacts, given there is only one wild population unit remaining. Spring Chinook Salmon NMFS estimates that historically there were up to 600,000 wild spring Chinook adults returning to the Central Valley and its tributaries.
From page 115...
... . The NMFS recovery plan explicitly identifies hatchery effects as a major stressor contributing to the decline of Central Valley steelhead.
From page 116...
... stressed hatchery risks and argued that releasing large numbers of hatchery fish could adversely affect wild Chinook salmon and steelhead through various mechanisms such as hybridization, competition between hatchery and wild fish for food and other resources, predation by hatchery fish on juvenile wild fish, and the effects on wild fish of increased fishing pressure as a result of increased hatchery production. Brannon et al.
From page 117...
... (The HSRG began a review of the Klamath River and Central Valley systems in 2010; reports were not yet available in early 2012.)
From page 118...
... salmon populations, whether they might even be harming them, or whether other factors are affecting salmon so strongly that they overwhelm any good that hatcher ies might do. How do those conclusions apply to the steelhead and Chinook salmon of the Central Valley?
From page 119...
... The committee judges that adoption of HSRG guidelines under a unified hatchery management plan will reduce (but not eliminate) risk to wild populations from hatcheries, and probably represents the most viable option for maintaining populations of salmonids in the Central Valley unless or until other methods are found to increase the productivity of wild populations.
From page 120...
... . While the PDO is correlated with many west coast salmon stocks, a clear correlation with Central Valley Chinook salmon has not been found (Botsford and Lawrence 2002)
From page 121...
... . High temperatures and fish densities induced an outbreak of disease in Chinook salmon oversummering in Butte Creek and resulted in prespawning mortalities between 20 and 60 percent (NMFS 2009a)
From page 122...
... Multiple Stressors and the Pelagic Organism Decline The pelagic organism decline (POD) was the simultaneous decline beginning in 2002 of the abundance indices of delta smelt, longfin smelt, threadfin shad, and juvenile striped bass.
From page 123...
... Using the results of various studies, the overall POD synthesis efforts by the management team identified some potential drivers that were not strongly related to abundances, which helps to constrain the problem, and illustrates the difficulties in relating drivers to population dynamics of the fish species. Most recently, the view from the POD management team has evolved with more attention paid to the longer-term declines and the notion of an ecological regime shift superimposed on the effects of the multiple stressors.
From page 124...
... Anadromous Salmonids At least two forums have attempted to characterize and score the importance of various stressors on ESA-listed anadromous salmonids in the Central Valley; the NMFS Draft Recovery Plan and the Delta Conceptual Models22 for those species. The NMFS approach is very detailed and specific as to species and population unit, life stage, and river locale.
From page 125...
... , using molecular kinship analysis of various life stages in the upper Sacramento River, estimated that their results could be accounted for by as few as 10 to 28 spawning adults above the Red Bluff Diversion Dam each year. The Central Valley subpopulation
From page 126...
... migrate into the bay-delta system in winter months. Most adult sturgeon undertake spawning migrations up the Sacramento River beginning in March and reach upriver locations (adjacent to and above Red Bluff Diversion Dam)
From page 127...
... The risks stem from the sturgeon's high trophic position in the benthic food web, the importance of life stages most at risk from these reproductive toxicants, and the poor demographic compensational abilities of this long-lived, slowly reproducing species. Because the southern distinct population segment is listed under ESA, recovery action may extend beyond the San Francisco Bay Delta.
From page 128...
... (2009) for adult green sturgeon.
From page 129...
... (2010) focused on individual species and examined whether decreases in delta smelt, longfin smelt, juvenile striped bass, and threadfin shad abundance indices in the early 2000s were the continuation of longer-term trends (since the 1970s)
From page 130...
... (2012) reported the results of a third statistical analysis of delta smelt abundance indices and similar but not identical explanatory variables as Thomson et al.
From page 131...
... First, statistical evidence and models suggest that both flows and flow paths are critical to population abundance of many species in the bay delta. However, none of the statistical flow-abundance relations suggest the existence of thresholds (i.e., that if the position of X2 were to be allowed to remain far upstream for suitable [species-dependent]
From page 132...
... However, options for San Joaquin fish are less certain, because studies suggest that passage through the delta main channel and collection and transport at the pumps -- the two main passage options -- result in equally low survival. Entrainment effects of SWP and CVP pumping are likely large in some years and, thus, act as an episodic stressor that has a significant adverse effect on delta smelt population dynamics, although it is very difficult to quantify the effects in simple ways.
From page 133...
... Toxic pollutants such as selenium also appear to be significant stressors, especially for sturgeon, with San Francisco Bay and the San Joaquin River being the areas of greatest concern. With appropriate investments both nutrients and selenium issues can be better managed, probably to the benefit of both functioning and structure in the delta and the bay.
From page 134...
... The committee judges that adoption of recent conservation guidelines under a unified hatchery management plan will reduce (but not eliminate) risk to wild populations from hatcheries, and probably represents the most viable option for maintaining populations of salmonids in the Central Valley unless or until other methods are found to increase the productivity of wild populations.
From page 135...
... Given the diversity of the challenges presented by "stressors" to the bay delta, better integration of the governance structures and science-policy dialogue, as suggested in other chapters of this report, is another important ingredient in addressing the stressor issues. It is clear from consideration of the many stressors and their impacts that eliminating any one is unlikely to reverse declines in the listed species.
From page 136...
... 2007. Population status of North American green sturgeon, Acipenser medirostris.
From page 137...
... 2010. An ecosystem model of the Sacramento-San Joaquin Delta and Suisun Bay, California.
From page 138...
... 2004. Sacramento River winter-run Chinook salmon biennial report 2002-2003.
From page 139...
... 1997. The Status of Late-Fall and Spring Chinook Salmon in the Sacramento River Basin Regarding the Endangered Species Act.
From page 140...
... 2011. Reducing Methylmercury Ac cumulation in the Food Webs of San Francisco Bay and Its Local Watersheds.
From page 141...
... 2010. Long-term changes in nutrient loading and stoichiometry and their re lationships with changes in the food web and dominant pelagic fish species in the San Francisco Estuary, California.
From page 142...
... 1996. A 2000 yr record of Sacramento-San Joaquin River inflow to San Francisco Bay estuary, California.
From page 143...
... Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science 6(2)
From page 144...
... 2008b. Losses of Sacramento River Chinook salmon and delta smelt to entrainment in water diversions in the Sacramento-San Joaquin Delta.
From page 145...
... 2007. Framework for Assessing Viability of Threatened and Endangered Chinook Salmon and Steelhead in the Sacramento-San Joaquin Basin.
From page 146...
... F., 2010. Losses of Sacramento River Chinook Salmon and Delta Smelt to En trainment in Water Diversions in the Sacramento-San Joaquin Delta.
From page 147...
... 2009b. Public Draft Recovery Plan for Sacramento River Winter-run Chinook Salmon and Central Valley Spring-run Chinook Salmon and the Distinct Population Segment of Central Valley Steelhead.
From page 148...
... 2010. Estimating survival and migration route probabilities of juvenile chinook salmon in the Sacramento­San Joaquin River Delta.
From page 149...
... 2006. Forecasting selenium discharges to the San Francisco Bay-Delta Estuary: Ecological effects of a proposed San Luis Drain extension.
From page 150...
... 2008. Biological Assessment of the Continued Long-Term Operation of Central Valley Project and State Water Project.
From page 151...
... Juvenile Chinook salmon (Oncorhynchus tshawytscha) in and around the San Francisco Estuary.
From page 152...
... 1996. Historical and pres ent distribution of Chinook salmon in the Central Valley drainage of California.


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