Draft Programmatic Environmental Impact Statement/Environmental Impact Report
San Francisco Estuary Invasive Spartina Project: Spartina Control Program
April 2003

3.2    Water Quality

Water quality of the San Francisco Estuary, including the Bay and the surrounding flats and tidal marsh may be affected directly and indirectly by implementation of the Spartina Control Program. This section describes potential impacts, and defines mitigation measures that will reduce the impacts to water quality to less than significant levels.

3.2.1 Environmental Setting

This section describes existing water quality in the San Francisco Estuary and processes affecting it, and outlines the regulatory framework under which water quality is protected. Potential effects of treatment methods on water quality are evaluated, and mitigation measures are identified for potentially significant effects. The region of influence for impacts to water quality includes the tidal flats and marshes where treatment will occur, and the shallow tidal waters immediately adjacent to these areas.

Natural Processes Affecting Water Quality

Water quality within the San Francisco Estuary is connected to and affected by complex regional and local natural processes. Hydrologic relationships between the Pacific Ocean, the Estuary, and the many freshwater tributaries (including the Sacramento-San Joaquin River system) govern salinity levels in different portions of the Estuary and along the Bay margins. Variable natural factors such as tidal cycles, local winds, basin bathymetry, and salinity gradients interact with river flows and affect the circulation of Estuary waters through channels, Estuary margins, and bays, distributing nutrients, salt concentrations, and pollutants. Major processes affecting water quality are described below.

Tidal Cycles. The Estuary has two low tides and two high tides every 24.8 hours. During each tidal cycle, an average of about 1.3 million acre-feet of water, or 24 percent of the Bay and Delta's volume, moves in and out of the Golden Gate. On the flood (incoming) tide, ocean water moves through the Golden Gate and into the Estuary's southern and northern reaches, raising the water level at the end of the South Bay by more than eight feet, and raising the height of the Sacramento River at the upstream edge of the Estuary by about three feet. It takes about two hours for the flood tide to reach the end of the South Bay and eight hours to reach Sacramento.

Subregional Conditions. Suisun and North Bay subregions (see Figure 2-1) receive the majority of freshwater input from the Sacramento and San Joaquin River system. In the open bays, density-driven currents show ebb dominance of the surface water and flood dominance of the bottom water. Waters in these embayments are well oxygenated, with low- to moderate-salinity and high-suspended solids concentrations. Water residence time affects the abundance and distribution of many estuarine organisms, the amount of primary production by phytoplankton, and some of the chemical and physical processes that influence the distribution and fate of pollutants. During low flow periods of the year (late summer), the residence time of freshwater moving from the Delta to the ocean can be relatively long (on the order of months) compared to periods when outflow is very high (winter), when freshwater can move from the Delta to the ocean in days.

The Central Bay subregion is influenced by ocean waters that are cold, saline, and lower in total suspended sediment. Water quality parameters fluctuate less than in other sectors of the Bay due to the predominance of ocean water. Net exchanges of ocean and Bay waters depend on freshwater flow in the Bay, tidal amplitude, and longshore coastal currents.

Text Box:  
Figure 3.2-1. Locations and mean discharges for mu-nicipal wastewater treatment plants in South San Francisco Bay. Adapted from Schemel et al. 1999, based on Davis et al. 1991.
The southern part of San Francisco Bay receives less than 10 percent of the natural freshwater flow into the Bay, but the majority (>75 percent) of wastewater discharges. The largest flow is from San Jose, where approximately 120 million gallons per day (MGD) of treated wastewater are released into Artesian Slough, a tributary to Coyote Creek (Figure 3.2-1). This fresh water flow creates a local zone of brackish water in the otherwise saline tip if the South Bay. The rest of the South Bay, because it has so little freshwater input, is essentially a tidal lagoon with a relatively constant salinity (approximately the same as ocean water, 32 parts per thousand, ppt). South Bay waters are influenced by Delta outflow only during the winter months, when low-salinity water moves southward into the southern reach displacing the saline, denser water northward. In the summer months, however, South Bay currents are largely influenced by wind stress on the surface; northwest winds transport water in the direction of the wind, and the displaced water causes subsurface currents to flow in the opposite direction.

Currents and Circulation. Circulation patterns within the Bay are influenced by Delta inflows, gravitational currents, and tide- and wind-induced horizontal circulation. The cumulative effects of the latter three factors on net circulation within embayments tend to dominate over that of freshwater inflows except during short periods after large storm events (Smith 1987). Exchanges between embayments are influenced both by mixing patterns within embayments and by the magnitude of freshwater inflows (Smith 1987).

Currents created by tides, freshwater inflows, and winds cause erosion and transport of sediments. Tidal currents are usually the dominant form of observed currents in the Bay. Tidal currents are stronger in the channels and weaker in the shallows (Cheng and Gartner 1984). These processes enhance exchange between shallows and channels during the tidal cycle, and contribute significantly to landward mixing of ocean water and seaward mixing of river water. Also, the South Bay begins flooding while San Pablo Bay is still ebbing, making it possible for the South Bay to receive water from the northern reach (Smith 1987).

Tides have a significant influence on sediment resuspension during the more energetic spring tide when sediment concentrations naturally increase, and particularly during the ebbs preceding lower low water when the current speeds are highest (Cheng and McDonald 1994). Powell et al. (1989), however, observed no correlation between tidal cycle and suspended sediment loads or distribution in the South Bay. Their conclusion was that winds are the most important factor in resuspending sediments in the South Bay, and that sources of sediments are more important than transport of sediment resuspended from other parts of the Bay (Reilly et al. 1992).

Wind‑induced currents have a significant effect on sediment transport by resuspending sediments in shallow waters (Krone 1979; Cloern et al. 1989). An estimated 100 to 286 million cubic yards of sediments are resuspended annually from shallow areas of the Bay by wind‑generated waves (Krone 1974; SFEP 1992b).

Water Quality

Water quality in the San Francisco Estuary has improved significantly since the enactment of the California Water Quality Control Act (Porter-Cologne) in 1969 and the Clean Water Act in 1972. Nevertheless, the Estuary waters still carry significant loads of pollutants from human sources. Under Section 303(d) of the Clean Water Act, states were required to develop a list of water bodies that do not meet water quality standards; this list is referred to as the "303(d) list." This list defines low, medium, and high priority pollutants that require immediate attention by State and Federal agencies. Portions of the Estuary have high-priority 303(d) listings for a number of pollutants, including dioxin compounds, furan compounds, PCBs, mercury, copper, nickel, and exotic (plant and animal) species.

The most comprehensive information describing water quality in the Estuary comes from the Regional Monitoring Program managed by the San Francisco Estuary Institute (SFEI) and ongoing studies by the Interagency Ecological Program (IEP). In addition, numerous short-term studies that focus on specific sites, resources, or pollutants are conducted on a regular basis by researchers and entities conducting permit-specified monitoring of waste discharges. The primary water quality parameters discussed below are: temperature, salinity, dissolved oxygen (DO), pH, total suspended solids (TSS), turbidity, and pollutants.

Temperature. Water temperatures in the Estuary range from approximately 10C to 22C (50F to 71.6F). Temperatures are influenced by seasonal solar cycles and variable inputs of river and coastal ocean waters. Temperatures are typically at the higher end of this range along the Estuary margin during daylight hours as the influence of solar energy warms the water.

Salinity. The salinity of the Estuary varies spatially and temporally. Along the northern reach the salinity increases from the Delta to the Central Bay. At the mouth of the Sacramento River, for example, the mean annual salinity averages slightly less than 2 ppt; in Suisun Bay it averages about 7 ppt; and at the Presidio in Central Bay it averages about 30 ppt. In the South Bay, salinities remain at near-ocean concentrations (32 ppt) during much of the year, except in the vicinity of the San Jose wastewater outfall at Artesian Slough, where salinities are lessoned. During summer months in dry years, high evaporation rates may cause salinity in South Bay to exceed that of ocean water.

Seasonal changes in the salinity distribution within the Estuary are controlled mainly by the exchange of ocean and Estuary water, and by river inflow. River inflow has the greater influence on salinity distribution throughout most of the Estuary because inflow varies widely, while variations in ocean inputs are relatively small. In winter, high flows of freshwater from the Delta lower the salinity throughout the Estuary's northern reach. High Delta flows also intrude into South Bay, lowering salinity there for extended periods. In contrast, during the summer, when freshwater inflow is low, saline water from the Bay intrudes into the Delta. The inland limit of salinity intrusion varies greatly from year to year. In addition, channel dredging can increase gravitational circulation and enhance salinity intrusion (Nichols and Pamatmat 1988).

Dissolved Oxygen. Oxygen concentrations in estuarine waters are increased by the mixing action of wind, waves, and tides; photosynthesis of phytoplankton and other aquatic plants; and high DO in freshwater inflow. DO concentrations are lowered by plant and animal respiration, chemical oxidation, and bacterial decomposition of organic matter.

The Estuary's waters are generally well oxygenated, except during summer in the extreme southern end of the South Bay where concentrations are reduced by poor tidal mixing and high water temperature. Typical concentrations of DO range from 9 to 10 milligrams per liter (mg/l) throughout the Estuary during periods of high river flow, 7 to 9 mg/l during moderate river flow, and 6 to 9 mg/l during the late summer months when flows are the lowest. Unlike the 1950s and 1960s, when inadequately treated sewage and processing plant wastes depleted oxygen in parts of the Bay and Delta, today there are few reports of places in the Estuary where low oxygen concentrations adversely affect beneficial uses. Today, the lowest concentrations in the Estuary are typically observed in the extreme South Bay but, in some instances, DO levels in semi-enclosed embayments such as Richardson Bay can be much lower than in the main water body (SFEI 1994).

pH. The pH of the water in San Francisco Bay is relatively constant and typically ranges from 7.8 to 8.2[1].

Total Suspended Solids (TSS) and Turbidity. Turbidity and TSS are generally used as measures of the quantity of suspended particles. The distinction between the two terms lies mainly in the method of measurement. In general, higher TSS results in more turbid water.

Regions of maximum suspended solids occur in the North Bay in the null zone[2] (generally 50 to 200 mg/l, but as high as 600 mg/l TSS). The specific location of the null zone changes depending upon freshwater discharge from the Delta. TSS levels in the Estuary vary greatly depending on the season, ranging from 200 mg/l in the winter to 50 mg/l in the summer (Nichols and Pamatmat 1988; Buchanan and Schoellhamer 1995). TSS also varies with tidal stage and depth (Buchanan and Schoellhamer 1995). Shallow areas and channels adjacent to shallow areas have the highest suspended sediment concentrations. The Central Bay generally has the lowest TSS concentrations; however, wind‑driven wave action and tidal currents, as well as dredged material disposal and sand mining operations cause elevations in suspended solids concentrations throughout the water column.

Pollutants. Pollutant loading to San Francisco Bay has long been recognized as one of many factors that has historically stressed aquatic resources. Pollutants enter the aquatic system through atmospheric deposition, runoff from agricultural and urbanized land, and direct discharge of waste to sewers and from industrial activity.

The Bay's sediment can be both a source and a sink for pollutants in the overlying water column. The overall influx of pollutants from the surrounding land and waste discharges can cause increases in sediment pollutant levels. Natural resuspension processes, biological processes, other mechanical disturbances, dredging, and sediment disposal can remobilize particulate-bound pollutants.

Metals. Ten trace metals in the aquatic system and in waste discharged to the Bay are monitored on a regular basis. Total and dissolved fractions are sampled three times a year at Regional Monitoring Program (RMP) stations throughout the Estuary. Tables 3.2-1 and 3.2-2 present dissolved and total trace metal concentration ranges in Bay waters during 1998 (SFEI 1998).

Organic Pollutants. Three general types of trace organic contaminants, polycylic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and pesticides, are measured in San Francisco Bay water on a regular basis.

Water column concentrations of dissolved and total PAHs in 1998 ranged from 2.1 to 46 parts per trillion (pptr) and from 20 to 300 pptr, respectively (SFEI 1998). Total PCB concentrations in Bay waters during 1998 ranged from 70 to 7,000 parts per quadrillion (ppq), and were below the U.S. Environmental Protection Agency (U.S. EPA) 4-day (chronic toxicity) water quality criteria (30 pptr) (SFEI 1998). Dissolved PCB concentrations ranged from 12 to 930 ppq. Bay waters also contained measurable concentrations of chlorinated pesticides, including chlordanes and DDTs. Total chlordane concentrations ranged from 21 to 5,700 ppq, while total DDT concentrations ranged from 190 to 9,900 ppq (SFEI 1998).

A recent review of historical data from several sources found several previously unidentified organic contaminants in the San Francisco Estuary (SFEI 2002). In this study, p-nonylphenol, a common constituent in detergents and other household products, agricultural surfactants, and many industrial products, was identified in Sacramento and San Joaquin River water (at 19 ng/L and 5 ng/L, respectively), but it was not detected in Estuary water.

Sediment Quality

Sediment quality in the Estuary varies greatly according to the physical characteristics of the sediment, proximity to historical waste discharges, the physical and chemical condition of the sediment, and sediment dynamics that change with location and season. Generally, the level of sediment contamination at a given location will vary depending on the rate of sediment deposition, which varies with seasons and tides (Luoma et al. 1990). Chemical contaminant dynamics in an estuary are closely associated with the behavior of suspended and deposited sediments. The physical and chemical characteristics of sediments, and the bioavailability and toxicity of sediment-associated chemicals to aquatic organisms, are particularly important in determining their potential impact on environmental quality.

While pollutant loading to the Estuary from point and non-point sources has declined dramatically over the past two decades, and surface sediment contamination may be declining from historical highs, Bay sediments are still an important source and sink of pollutants. Much of the data documenting concentrations of trace metals and organics in Bay sediments are found in the historical summary of Long and Markel (1992) and in the more recent monitoring efforts by the State's Bay Protection and Toxic Cleanup Program (BPTCP) (SFBRWQCB 1994) and Regional Monitoring Program (SFEI 1994 and 1998).

Text Box: Table 3.2-3. Ranges of Trace Pollutants in San Francisco Bay Sediments (SFEI 1998)
	Minimum	Maximum	ER-L	ER-M
Arsenic	3.1	19	8.2	70
Cadmium	0.1	2.1	1.2	9.6
Chromium	63	216	81	370
Copper	8.5	76	34	270
Lead	5.4	65	46.7	218
Mercury	0.03	0.82	0.15	0.71
Nickel	68	228	20.9	51.6
Selenium	0.06	0.52		
Silver	ND	2.0	1.0	3.7
Zinc	64	256	150	410
TOTAL PAHS	0.033	6.30	4.022	44.792
Total PCBs	ND	0.26	0.0227	0.18
Total DDTs	No Data	0.00158	0.0461
Total Chlordanes	ND	0.0099	0.0005	0.006
Key: 	Concentrations bolded exceed the Lowest Observable Effects Level (ER-L)
	Concentrations bolded and underlined exceed the Median Observable Effects Level (ER-M)
	ND  Not detectable at laboratory limits
Concentrations of Metals and Organic Pollutants in Sediments. Mean concentrations of trace metals and organics in sediments vary according to grain size, organic carbon content, and seasonal changes associated with riverine flow, flushing, sediment dynamics, and anthropogenic inputs. Anthropogenic inputs appear to have the greatest effect on sediment levels of copper, silver, cadmium, and zinc, as well as several chlorinated and petroleum hydrocarbons (SFBRWQCB 1994). Ranges in sediment metals and trace organic concentrations during 1998 are listed in Table 3.2-3. The table also compares measured concentrations to effects range-low (ER-L) and effects range-median (ER-M) values, which are levels that are rarely associated with adverse effects to benthic organisms from exposures to sediment-associated contaminants and levels that are frequently associated with adverse impacts, respectively (Long et al., 1995). For most pollutants, ranges in measured concentrations exceed the respective ER-L values but are below the corresponding ER-M values. The exceptions are mercury, nickel, total PCBs, and total chlordanes, which exceed the ER-M values at one or more locations in the Bay. Some sites within San Francisco Bay, such as Lauritzen Canal, the Port of Oakland near San Leandro Bay, and Richmond Harbor, which have been greatly affected by historical contamination, contain sediment pollutant levels which are considerably higher than those measured by the Regional Monitoring Program.

3.2.3 Analysis of Potential Effects

Significance Criteria

The San Francisco Bay Area Regional Water Quality Control Board and the Central Valley Regional Water Quality Control Board (Water Boards) are the primary agencies responsible for protecting water quality in natural waters ("waters of the State"). The Water Boards' Basin Plans[3] designate beneficial uses for each water body (including wetlands and marshes) in the San Francisco Bay and Sacramento Regions (Table 3.2-4), and set water quality objectives to protect the present and potential beneficial uses. In addition, the Basin Plans identify a number of numerical and narrative objectives for surface waters that apply to all waters within the Regions. The surface water objectives include goals for a wide range of factors, including DO, pH, sediment, toxicity, and biota population and community ecology. The Basin Plan includes an implementation plan for achieving the water quality objectives for each of the Regions' water bodies. The designated beneficial uses, combined with the narrative and numerical water quality objectives and the implementation plan constitute water quality standards for the San Francisco Bay and Central Valley Regions. The Water Boards have also been designated as the State agencies responsible for implementing the Federal National Pollutant Discharge Elimination System (NPDES) under Section 401 of the Clean Water Act.

Text Box: Table 3.2-4. Beneficial Uses of Waters of the San Francisco Estuary as Defined by the San Francisco Bay Area Regional Water Quality Control Board
	Central San Fran-cisco Bay	Lower San Francisco Bay	South San Francisco Bay	San Pablo Bay	Suisun Bay
Industrial Service Supply	E	E	E	E	E
Industrial Process Supply	E				
Navigation	E	E	E	E	E
Commercial and Sport Fishing	E	E	E	E	E
Shellfish Harvesting	E	E	E	E	
Contact Recreation	E	E	E	E	E
Non-contact Recreation	E	E	E	E	E
Fish Spawning	E		P		E
Fish Migration	E	E	E	E	E
Estuarine Habitat	E	E	E	E	E
Rare and Endangered Wildlife Habitat	E	E	E	E	E
Wildlife Habitat	E	E	E	E	E
Key: E = Existing, P = Potential

Text Box: Table 3.2-5. Water Quality Criteria for Selected Constituents

Constituent	California Toxics Rule Criteriaa
Saltwater	California Ocean Planb
Marine Aquatic Life	Drinking Waterc 
State & US
mg/L	CCCe
mg/L	Daily Maximum
mg/L	Instantaneous Max
mg/L	MCL
Copperd	4.8	3.1	12	30	1,300
Leadd	210	8.1	8	20	15
Mercuryd	Reservedf	Reservedf	0.16	0.4	2
Seleniumd	290	71	60	150	50
PCBs	NA	0.03	NA	NA	0.5
Glyphosate	NA	NA	NA	NA	700
a.	Enclosed Bays and Estuaries criteria are the same as CTR criteria for all listed constituents.
b.	California Ocean Plan criteria provided for comparison.
c.	State and USEPA drinking water maximum contamination levels (MCLs) are provided for comparison only.
d. 	Criteria apply to California waters except for those waters subject to objectives in Tables III-2A and III-2B of the San Francisco Re-gional Water Quality Control Board's (SFRWQCB) 1986 Basin Plan, that were adopted by the SFRWQCB and the State Water Re-sources Control Board, approved by EPA, and which continue to apply. 
e. 	Criteria Maximum Concentration (CMC) equals the highest concentration of a pollutant to which aquatic life can be exposed for a short period of time without deleterious effects. Criteria Continuous Concentration (CCC) equals the highest concentration of a pollutant to which aquatic life can be exposed for an extended period of time (4 days) without deleterious effects. mg/L equals micrograms per li-ter.
f.	U.S. EPA did not establish a standard at time of promulgation, but may do so at a future time.
NA  Criteria not available.

The California Toxics Rule (CTR). In May 2000, U.S. EPA promulgated water quality criteria for priority toxic pollutants for California's inland surface waters and enclosed bays and estuaries. Included are both human health and aquatic life protective criteria. The CTR criteria, along with the beneficial use designations in the Basin Plans, are directly applicable water quality standards for these toxic pollutants in these waters. Implementation provisions for these standards are provided in the Policy for Implementation of Toxics Standards for Inland Surface Waters, Encloses Bays, and Estuaries of California (SWRCB Resolution No. 2000-015). The CTR and other criteria for selected pollutants are listed in Table 3.2-5.

U.S. EPA also published recommended water quality criteria for nonylphenols for protection of saltwater aquatic life. The recommended criteria for continuous concentration (4-day) average and maximum concentration (1-hour average) are 1.6 g/L and 6.2 g/L, respectively.For the purposes of this evaluation, significant impacts to water quality would be determined to occur if the project would:

 Violate any Federal, State, regional, or local water quality standard, or any waste discharge requirement or NPDES permit condition;

• Discharge any toxic substances into the water in concentrations that are lethal to or that produce significant alterations in population or community ecology or receiving water biota;

• Degrade the existing high quality of water in any waters of the State; or

Otherwise degrade water quality and adversely affect beneficial uses.

This section primarily evaluates possible impacts that would directly affect water quality and result in a violation of a numerical water quality standard or permit condition. Other, more subtle potential impacts, such as alteration of community ecology or adverse impact to a beneficial use of wetland or estuarine habitat, are evaluated in Section 3.3, Biological Resources.

The primary water quality impacts associated with the treatment of non-native cordgrass are summarized in Table 3.2-6. Each impact is described below, followed by an assessment of the significance of the impact. Mitigation measures that would be applied are identified in the text and summarized in Table 3.2-7.

ALTERNATIVE 1:    Proposed Action/Proposed Project - Regional Eradication Using All Available Control Methods

Impacts to water quality from physical and chemical treatment methods could be associated with application of herbicides, remobilization of sediment contaminants, spills of petroleum products (required for machinery, vehicles, and boats) or herbicides, and erosion of marsh sediments in the vicinity of structures.

IMPACT WQ-1: Degradation of Water Quality Due to Herbicide Application

Treatment methods involving the use of herbicides may degrade water quality and subsequently affect beneficial uses of waters of the Bay.

Only one herbicide, glyphosate, has been approved for use by the U.S. EPA in estuarine environments. The commercial glyphosate products that will be used by the Control Program are Rodeo and Aquamaster. Glyphosate must be combined with a suitable surfactant and colorant, as described in Chapter 2, Program Alternatives. The following presentation of empirical information on water quality impacts from herbicide applications is focused on Rodeo or Aquamaster, the active ingredient (glyphosate), its breakdown products, the surfactants R-11, LI 700, and Agri-dex, and the colorant, Blazon Blue.

Glyphosate. Rodeo and Aquamaster are simple aqueous solutions of isopropylamine salt, and contain no inert ingredients other than water. The primary decomposition product of glyphosate is aminophosphoric acid (AMPA), and the commercial product contains an impurity, N-nitrosoglyphosate (NNG). The potential effects of AMPA and NNG are encompassed by the available toxicity data on glyphosate and glyphosate formulations (SERA 1996). Glyphosate is water-soluble and may be transported by surface waters. It is stable in water and sunlight, but is degraded rapidly by bacteria. Specific degradation rates in water depend on temperature and pH, and are usually within days to weeks. It is considered moderately persistent in soils with an estimated half-life of 47 days. Because glyphosate adheres strongly to particles, it does not readily leach to waters (Sprankle et al., 1977 cited in Albertson, 1998), and potential movement of glyphosate to groundwater is unlikely. Information concerning the mobility, persistence, and toxicity of glyphosate in estuarine environments is compiled in Appendix E-1.

Surfactants. Pursuant to the U.S. EPA registration label for glyphosate, a non-ionic surfactant is required whenever glyphosate is used in aquatic systems. Several non-ionic surfactant formulations are registered by the U.S. EPA and the California Department of Pesticide Regulation for use in aquatic systems. Agridex, R-11, and LI-700 have been selected for use by the Control Program as among the least toxic of the approved surfactants. These three surfactants are described briefly below. Product labels and additional information are provided in Appendix E-2.

Agri-dex (Helena Chemical Company) is a non-ionic surfactant consisting of a paraffin base petroleum oil, polyol fatty acid esters, and polyethoxylated derivatives of the fatty acid esters. The pesticide label identifies a toxicity category of 3-4 (CAUTION)[4]. This surfactant improves pesticide application by modifying the wetting and deposition characteristics of the spray solution resulting in a more even and uniform coverage. The ingredients in this surfactant break down within several days.

R-11 Spreader Activator (Wilbur-Ellis Company) consists of a non-ionic alkylphenol ethoxylate. The pesticide label identifies a toxicity category of 3-4 (CAUTION). This surfactant increases the efficacy of herbicides by facilitating wetting and uniform coverage over the target surface.

Alkylphenol ethoxylates are widely used as detergents, emulsifiers, solubilizers, wetting agents, and dispersants, and are introduced into the aquatic environment primarily through industrial and municipal wastewater discharges (Heinis et al. 1999). Depending on the environment, alkylphenol ethoxylates may break down into a variety of metabolites, some of which may persist in the water column for several weeks and in sediments for many years (Ferguson et al. 2001). One of the break-down products, nonylphenol, has been found to bioaccumulate (Ferguson et al. 2001) and to have estrogenic effects on some organisms (Dreze et al. 2000, Meregalli et al. 2001).

Because the primary contributors of nonylphenol to the environment are wastewater sources, most of the available information on the persistence and effects of these substances is focused on wastewater processes. Several studies have concluded that nonylphenol does not tend to be persistant (i.e., it breaks down further to inert products) under aerobic conditions (J. Maguire 1999, Staples et al. 1998).

LI-700 Penetrating Surfactant (Loveland Industries), contains phosphatidylcholine (lecithin), which is a naturally occurring lipid that biodegrades readily. It also contains methylacetic acid and alkyl polyoxyethylene ether. The pesticide label identifies a toxicity category of 1 (DANGER). This surfactant facilitates uniform coverage of the spray solution and aids in penetration of the herbicide. The ingredients in this surfactant break down within several days.

Colorant. Blazon Spray Pattern Indicator (Milliken Chemical) is a water-soluble polymeric colorant. As with most colorant products, the active ingredients are proprietary; the Material Safety Data Sheet indicates that it is non-hazardous and non-toxic. The product information sheet reports that the product is non-staining to the skin or clothing. A literature survey on the toxicity of color indicators done for the U.S. Department of Agriculture reports "most commercial indicators are blue and most often a form of Acid Blue 9" (McClintock 1997 and Zullig 1997 cited in SERA 1997b). Acid Blue 9 is a disodium salt classed chemically as a triphenelmethane color (SERA 1997b). The Cosmetic, Toiletry, and Fragrance Association (CTFA) name for certified batches of Acid Blue 9 is FD&C blue No. 1. Product information for Blazon Spray Pattern Indicator is provided in Appendix E-2.

Herbicide mixtures. The glyphosate/surfactant/colorant mixture is a chemical formulation, and the toxicological characteristic may vary from that of its constituents. While information about the constituents may be instructive, it is desirable to consider the characteristics of the combined mixture to accurately assess possible toxicity. There is a wide range of possible interactions between the glyphosate mixture constituents, and the effects are difficult to predict based on structural, mechanistic, or theoretical considerations (SERA 1997b). Studies of toxicity of glyphosate mixtures in saline or estuarine environments are few, and data are unreliable. The Control Program will perform studies, including bioassays, during the early phases of the Program to determine if there are additional toxic effects of the herbicide mixtures.

Herbicide application. Impacts to water quality from herbicide application depend on environmental fate, degradation rates of active agents and decomposition products of the herbicides. The primary route by which herbicide solution may contact water is by overspray directly onto the water surface, or by washing off from plants due to precipitation or tidal inundation.

Glyphosate mixtures may be applied as sprays to plant surfaces, pastes applied to cut stems, or solutions wiped or painted on foliage. Spray mixtures may be administered from manually transported tanks (backpack sprayers) or spray equipment mounted on trucks, track vehicles, boats, or helicopters (broadcast sprayers; see Chapter 2, Program Alternatives, Alternative 1 for a complete description of application methods and restrictions). Manual application would entail workers walking through the marsh and applying herbicide directly to target plants, with limited overspray to surrounding plants or water surfaces. Application from a boat would also result in direct application of herbicide to target plants, with limited overspray. Application from trucks and track vehicles would entail vehicles moving through the marsh, either on roadways and levees or tracking over marsh vegetation, respectively applying herbicide more broadly to vegetation in the immediate area. Aerial application would be by helicopter with either a boom sprayer (a horizontal pipe with spray nozzles along its length, mounted to the bottom of the helicopter) or a spray ball (a hollow ball with perforations suspended from the bottom of the helicopter). Aerial application would result in a wider dispersion of herbicides, with greater potential for overspray onto non-target areas or the water surface. Aerial application is would be used infrequently, and primarily at large areas of dense cordgrass infestations, particularly in locations where little native cordgrass and other non-target plants are nearby. The rate of application for each type of treatment was provided in Table 2-2.

Herbicide mixtures may be indirectly discharged to surface waters by tidal action or rainfall that rinses the herbicide solution from the plants. Rainfall is unlikely to occur during the planned application season (late summer), and herbicide applications would be postponed if rainfall were predicted, but tidal inundation is inevitable in many locations on a regular cycle.

Energetic tidal cycles and tidal currents effectively disperse bound (adsorbed) glyphosate and surfactants and dilute them in microbially active suspended sediment. Studies of the fate of glyphosate and surfactants applied in tidal marshes and mudflats have reported that concentrations of both substances dropped below detection levels as soon as two tidal cycles (one day) to seven days (Kroll 1991, Paveglio et al. 1996) after application. The initial tidal submergence of sprayed surfaces disperses a large fraction of applied glyphosate and surfactant.

Research in Willapa Bay, Washington, found that the highest average maximum concentrations of glyphosate and X-77 Spreader surfactant in water dispersed from sprayed estuarine mud with the first flooding tide were 26 mg/L and 16 mg/L, respectively. These conditions represent the highest expected concentrations for exposure for aquatic invertebrates or fish swimming into freshly sprayed sites. The solution of Rodeo (3.8 pts/acre) and X-77 Spreader (0.9 pts/acre) was applied aerially (Paveglia et al. 1996). This "worst case" concentration of glyphosate and surfactants is inherently short-lived in high-energy tidal environments, and would not be pertinent to potential chronic, low-level effects. The same study found that concentration of glyphosate and surfactants were below analytic detection limits (0.5 ppb) during the first high tide after treatment. Kroll (1991) found that glyphosate concentrations in seawater were below the detection limit of 5 ppb within 7 days after treatment by Rodeo (0.75% solution) and Arborchem Aquatic surfactant (0.5% solution) by a hand-held sprayer.

Research conducted for the California Department of Food and Agriculture (Trumbo 2002) studied the environmental fate and aquatic toxicity of Rodeo and R-11 in three locations, including a Sacramento-San Joaquin Delta slough, a riverine area, and a no-outlet pond. This study measured glyphosate, amino methyl phosphonic acid (AMPA; glyphosate's primary metabolite), nonylphenol ethoxylate, and nonylphenol at treated sites one hour, two days, and eight days after application. The study also tested for toxicity using 96-hour toxicity tests with the fish species fathead minnow Pimephales promelas. The study found that concentrations of the tested constituents at slough and river sites (with moving water) was below detectible levels for all tests, and that there was no significant mortality of test fishes. The pond site, however, showed detectable residues of glyphosate, nonylphenol ethoxylate, and nonylphenol at one hour and two days after treatment, but all constituents were below detection limits by day eight. The one-hour pond samples experienced 30% mortality of test fishes, which, because of the relatively low concentrations of glyphosate (which is known to be non-toxic at the detected level), was attributed to effects caused by nonylphenol ethoxylate and nonylphenol. The two- and eight-day tests showed no significant mortality to test fishes.

Kilbride et al. (2001) conducted another study in Willapa Bay to evaluate the fate of a more concentrated glyphosate mixture (5% Rodeo solution and 2% LI-700 solution) in sediments. This concentration is above that permitted for manual application to cordgrass. Both mudflat plots and cordgrass plots were treated. Sediment samples were collected at 1 and 21 days, and at one year after treatment, and geometric mean concentrations ranged from 0.090 mg/kg to 2.30 mg/kg.

Patten (2002) compiled data on the fate of glyphosate in water and sediment following applications in estuarine environments. Data are presented as geometric means for immediate maximum concentration (<3hrs after application) and short-term concentration (between24 hrs and 48 hrs after application). For use rates between 8 and 16 kg/ha (7-15 lbs/acre), the immediate maximum geometric mean glyphosate concentrations were 0.174 mg/L (174 mg/L) in water and 2 mg/kg in sediment. The short-term geometric mean glyphosate concentrations were 0.003 mg/L (3 mg/L) in water and 1.9 mg/kg in sediment[pro1] .

These independent lines of research in the fate of glyphosate and surfactants in tidal (and other) habitats suggest that potential impacts to water quality and beneficial uses of waters of the State caused by spraying glyphosate mixtures in intertidal environments are likely to be small and temporary. Therefore, controlled applications (i.e., following label instructions) of registered herbicides are not expected to degrade water quality, except for limited temporal and spatial extent.

Herbicides adsorbed by soils also degrade rapidly in the environment. Glyphosate has little potential for affecting groundwater because of its strong affinity for soil particles, which results in low mobility in soils. Following herbicide application and eventual decay of affected plant roots, local soils may be somewhat destabilized and subject to erosion prior to recolonization, but this would not facilitate transfer of glyphosate adsorbed to soil particles to the underlying groundwater aquifer.

In summary, the use of glyphosate and surfactants to treat infestations of non-native cordgrass would result in less than significant impacts on water quality due to the rapid degradation rate and controlled application of herbicides only on target plants[pro2] . Since application of herbicides would take place during low tide and low wind conditions, the herbicide would likely be absorbed by plants for a minimum of several hours (up to several weeks or months in high marsh) following application resulting in less than significant quantities of glyphosate or surfactants entering the water.

MITIGATION WQ-1: Herbicides shall be applied directly to plants and at low or receding tide to minimize the potential application of herbicide directly on the water surface. Herbicides shall be applied by a certified applicator and in accordance with application guidelines and the manufacturer label.

The Control Program shall obtain coverage under the State NPDES Permit for the Use of Aquatic Herbicides and any necessary local permits. A monitoring program shall be implemented as part of the NPDES permit, and shall include appropriate toxicological studies to determine toxicity levels of the herbicide solutions being used. The Control Program shall use adaptive management strategies to refine herbicide application methods to increase control effectiveness and reduce impacts. The Control Program shall continue to investigate improved herbicide formulations with lower ecological risk.

IMPACT WQ-2: Herbicide Spills

Large volumes of herbicide or surfactant, spilled or misapplied, could degrade water quality and cause temporary toxicity. As described for Impact WQ-1, above, controlled applications (i.e., following label instructions) of registered herbicides are not expected to degrade water quality because these materials degrade rapidly in the environment and do not represent high potentials for toxicity or bioaccumulation in marine or terrestrial organisms. However, if large volumes of herbicide or surfactant (adjuvant) are to be spilled near the treatment site in an undiluted (neat) form, or misapplied, these events would degrade water quality and cause temporary toxicity. Thus, impacts to water quality associated with large volume spills would be potentially significant.

MITIGATION WQ-2: Herbicides shall be applied by or under the direct supervision of trained, certified or licensed applicators. Storage of herbicides and adjuvants/surfactants on-site shall be allowed only in accordance with an approved spill prevention and containment plan; on-site mixing and filling operations shall be confined to areas appropriately bermed or otherwise protected to minimize spread or dispersion of spilled herbicide or surfactants into surface waters.

IMPACT WQ-3: Fuel or Petroleum Spills

Spills of gasoline or other petroleum products, required for operation of motorized equipment, into or near open water could degrade water quality, with potential for toxicity or contaminant bioaccumulation.

Gasoline or other petroleum products, such as oil and hydraulic fluids, required for operation of motorized equipment, could spill into or near open water. Large spill volumes could degrade water quality, with potentials for toxicity and contaminant bioaccumulation in marsh organisms. Water quality impacts also may occur if ignition fluids such as gasoline used for burning were inadvertently sprayed or spilled to surface waters. Gasoline, diesel, and other distilled petroleum products are more water-soluble than crude oils and heavier distillate fractions. However, they are also more volatile and therefore lost rapidly from water to the atmosphere. The lower molecular weight aromatic hydrocarbon compounds in petroleum products can be toxic to marine organisms at low exposure concentrations. Consequently, some toxicity to marine organisms could occur in the immediate vicinity of a spill, whereas environmental weathering processes reduce the toxicity of the spill with time.

This impact to water quality is potentially significant, but would be localized to the general vicinity of the spill and temporary. Impacts related to spills generally can be reduced to less-than-significant levels by implementing specific mitigation measures and best management practices.

MITIGATION WQ-3: Fueling operations or storage of petroleum products shall be maintained off-site, and a spill prevention and management plan shall be developed and implemented to contain and clean up spills. Transport vessels and vehicles, and other equipment (e.g., mowers, pumps, etc.) shall not be serviced or fueled in the field except under emergency conditions; hand-held gas-powered equipment shall be fueled in the field using precautions to minimize or avoid fuel spills within the marsh. Other, specific best management practices shall be specified as appropriate in project-specific Waste Discharge Requirements.

IMPACT WQ-4: Contaminant Remobilization

Treatment methods that include dredging or excavation of anaerobic bay mud may expose buried sediments with higher levels, or more biologically available forms of heavy metals (e.g., mercury, nickel, and zinc) or other contaminants such as polychlorinated biphenyls (PCBs). As shown in Table 3.2-3, heavy metals, including mercury, are present in bay muds from natural and artificial sources. Background levels in the San Francisco Bay are very high for some of these constituents compared to most estuaries nationally. If dredging or excavation is done in areas with high concentrations of metals or pollutants, it could degrade water quality and contribute to exposure of marsh organisms. Remobilization of contaminant would not be likely to occur from treatment methods that do not directly disturb sediments. Treatment methods that entail constructing levees or projects that require constructing roads for access could expose contaminants and create a minor risk to water quality.

MITIGATION WQ-4: For projects where dredging or excavation methods are used, a preliminary assessment shall be performed to determine the potential for contamination in sediments prior to initiating treatment. The preliminary assessment shall include (1) review of existing site data (e.g., from Regional Monitoring Program) and (2) evaluation of historical site use and/or proximity to possible contaminant sources. If the preliminary assessment finds a potential for historic sediment contamination, an appropriate sediment sampling and analysis plan shall be developed and implemented. If contaminants are present at levels of possible concern (but below levels that might trigger site cleanup), an alternative treatment method (that shall not disturb sediment) will be implemented, or the project shall apply to the Regional Water Board for site-specific Waste Discharge Requirements. If significant contamination that warrants site cleanup is found, sampling information shall be turned over to the U.S. Environmental Protection Agency or other appropriate authority.

ALTERNATIVE 2: Regional Eradication Using Only Non-Chemical Control Methods


Impacts to water quality from individual treatment methods and combinations of methods generally would be the same as those described for Alternative 1, with the exception that potential impacts associated with herbicide application and spills would be replaced by increased contaminant remobilization and erosion due to repeated application of physical or mechanical methods and ground disturbance. Overall, impacts to water quality are considered less than significant and subject to feasible mitigation.

Mitigation Measures

Mitigation measures WQ-3 and WQ-4 also apply to this alternative.

ALTERNATIVE 3: No Action - Continued Limited, Regionally Uncoordinated

Under Alternative 3, all types of control methods would continue to be used in the Estuary as needed by individual landowners, without benefit of training and standardization provided by the Spartina Control Program. Water quality impacts from herbicide application and resuspension of contaminants would still occur. Water quality impacts from herbicide and fuel spills might occur with disproportional frequency as a result of a lack of training and application standards.

Mitigation Measures

Mitigation measures WQ1, WQ-2, WQ-3 and WQ-4 would apply to this alternative.

Impact WQ-5: Water Quality Effects Resulting from Sediment Accretion

Colonization by invasive cordgrass can directly and indirectly affect water quality by trapping marsh sediments (Daehler and Strong, 1996). This process filters suspended particles from marsh waters, thereby increasing water clarity and light penetration, and promoting further deposition and accumulation of sediment and possible changes in sediment texture (Daehler and Strong, 1996). Accretion rates vary but appear to be related to stem density and sediment supply, and inversely related to wind and wave action (Chung, 1985 cited in Ebasco 1997). Sediment accretion and stabilization may eventually alter local topography and habitats relative to tidal elevation, promote changes in tidal drainage channels, and change topography from gentle slope to steep slopes in tidal channels. Changes in marsh circulation can, in turn, decrease the frequency of tidal inundation or exchange, and lead to stagnation and localized degradation of water quality. Spartina colonization of flood control channels may also increase flooding potential of residential and commercial properties (see also Section 3.1-Geomorphology and Hydrology). These indirect effects would result in potentially significant impacts to water quality.

This alternative is not expected to affect water quality standards although some beneficial uses associated with fish and wildlife habitat may be adversely affected. Other, local control programs, independent of the proposed regional eradication program, could generate waste discharges and affect local water quality conditions; however evaluation of local control programs is outside the scope of this EIS/EIR.

MITIGATION WQ-5: No feasible mitigation has been identified to address this impact. Moreover, mitigation measures associated with treatment methods would not be implemented by the Conservancy or the Service or required under this alternative. Locally sponsored control programs may incorporate mitigation measures to reduce potential impacts on water quality and sediment accretion.

Residual Impacts

Because no mitigation measures would be implemented, residual impacts would be as described above. These residual impacts are considered potentially significant.

View Table 3.2-6:   Summary of Potential Water Quality Effects
View Table 3.2-7: Summary of Mitigation Measures for Water Quality

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[1] Water or solutions that are acidic have a pH of less than 7.0, and basic or alkaline water have a pH greater than 7.0. A pH of 7.0 is considered neutral.

[2] The null zone is area or region of an estuary where the bottom, high-density and surface, low-density currents have equal and opposite effects. It is defined as the zone where the mean near-bottom speed is zero. The actual location of the null zone migrates in response to changes in river discharge. It is important because it is typically characterized by high concentrations of suspended particulate matter and rapid sediment accumulation.

[3]         San Francisco Regional Water Quality Control Board (Region 2) Water Quality Control Plan (1995) and Water Quality Control Plan for the Sacramento and San Joaquin River Basins (Region 5; 1998)

[4]          Toxicity categories are determined by the U.S. EPA for human health affects. See http://www.epa.gov/oppfead1/labeling/lrm/chap-08.htm for more information on pesticide label requirements.

 [pro1]Need to compare planned projects (application rates, etc) to these studies).

 [pro2](would be helpful to provide some estimate of spatial and temporal effects to water quality (DO and turbidity) in order to help determine significance)