7. Dredging & Dredged Spoil Disposal:

Dredging is associated with improving river navigation for commercial and recreational activities and for maintaining the navigation channels of ports and marinas. Dredging may also be carried out during the construction of roads and bridges and the placement of pipe, cable, and utility lines. Dredging is also conducted to maintain channel flow capacity for flood control purposes.

Dredging results in the temporary elevation of suspended solids emanating from the project area as a turbidity plume. Excessive turbidity can affect salmon or their prey by abrading sensitive epithelial tissues, clogging gills, decreasing egg buoyancy (of prey), and affects photosynthesis of phytoplankton and submerged vegetation leading to localized oxygen depression. Suspended sediments subsequently settle, which can destroy or degrade benthic habitats (NMFS 1997).

The removal of bottom sediments during dredging operations can disrupt the entire benthic community and eliminate a significant percentage of the feeding habitat available to fish for a significant period of time. The rate of recovery of the dredge area is temporally and spatially variable and site specific. Recolonization varies considerably with geographic location, sediment composition, and types of organisms inhabiting the area (Kennish 1997). Dredging may also affect the migration patterns of juvenile salmonids as a result of noise, turbulence, and equipment (FRI 1981).

The suspended sediments dredged from estuarine and coastal marine systems are generally high in organic matter and clay, both of which may be biologically and chemically active. Dredged spoils removed from areas proximate to industrial and urban centers can be contaminated with heavy metals, organochlorine compounds, polyaromatic hydrocarbons, petroleum hydrocarbons, and other substances (Kennish 1997) and thereby prone to resuspension. Sediments in estuaries downstream from agricultural areas may also contain herbicide and pesticide residues (NMFS 1997).

Dredging and subsequent sediment deposition poses a potential threat to the eelgrass ecosystems in estuaries, which provide important structural habitat and prey for salmon (see estuary alteration section, below). Dredging not only removes plants and reduces water clarity, but can change the entire physical, biological, and chemical structure of the ecosystem (Phillips 1984). Dredging also can reverse the normal oxidation/reduction potential of the sediments of an eelgrass system, which can reverse the entire nutrient-flow mechanics of the ecosystem (Phillips 1984).

Concomitant with dredging is spoil disposal. Dredged material disposal has been used in recent years for the creation, protection and restoration of habitats (Kennish 1997). When not used for beneficial purposes, spoils are usually taken to marine disposal sites and this in itself may create adverse conditions within the marine community. When contaminated dredged sediment is dumped in marine waters, toxicity and food-chain transfers can be anticipated, particularly in biologically productive areas. The effects of these changes on salmon are not known.

Conservation Measures -- Dredging & Dredged Spoil Disposal:

Below are the types of measures that can be undertaken by the action agency on a site-specific basis to conserve salmon habitat in spawning redds, eelgrass beds and other EFH areas of particular concern, that have the potential to be affected by dredging/spoil disposal activities. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat. The following suggested measures are adapted from NMFS (1997), NMFS (1997d), and Meyer (1997 personal communication).

8. Estuarine Alteration:

Estuaries represent transitional environments coupling land and sea water. The dominant features of estuarine ecosystems are their salinity variances, productivity, and diversity, which, in turn are governed by the tides and the amount of freshwater runoff from the land. These systems present a continuum along a fresh-brackish-salt water gradient as a river system empties into the sea. Estuarine ecosystems, containing a large diversity of species that reflect the great structural diversity and resultant differentiation of niches, may be characterized as:

In Oregon and Washington where there are relatively few estuarine wetlands because of the steep topography of the shore, it is estimated that between 50% and 90% of the tidal marsh systems in estuaries have been lost this century (Frenkel and Morlan 1991). The estuarine environment benefits salmon by providing a food rich environment for rapid growth, physiological transition between fresh and salt water environments, and refugia from predators (Simenstad 1983). Estuarine eelgrass beds, macroalgae, emergent marsh vegetation, marsh channels, and tidal flats provide particularly important estuarine habitats for the production, retention and transformation of organic matter within the estuarine food web as well as a direct source of food for salmon and their prey. Additionally, estuarine marsh vegetation, overhanging riparian vegetation, eelgrass beds, and shallow turbid waters of the estuary provide cover for predator avoidance. Estuaries provide enough habitat variety to allow the numerous species and stocks of salmonids to segregate themselves by niche.

Chinook salmon fry, for example, prefer protected estuarine habitats with lower salinity, moving from the edges of marshes during high tide to protected tidal channels and creeks during low tide (Healey 1980, 1982; Levy and Northcote 1981, 1982; Kjelson et al.1982; Levings 1982). As the fish grow larger, they are increasingly found in higher salinity waters and increasingly utilize less-protected habitats, including delta fronts or the edge of the estuary before dispersing into marine waters. As opportunistic feeders, chinook salmon consume larval and adult insects and amphipods when they first enter estuaries, with increasing dependence on larval and juvenile fish such as anchovy, smelt, herring, and stickleback as they grow larger (Sasaki 1966; Dunford 1975; Birtwell 1978; Levy et al. 1979; Northcote et al. 1979; Healey 1980,1982; Kjelson et al. 1982; Levy and Northcote 1981; Levings 1982; Gordon and Levings 1984; Myers 1980; Reimers 1973).

For juvenile coho, large woody debris is an important element of estuarine habitat (McMahon and Holtby 1992). During their residence time in estuaries, coho salmon consume large planktonic or small nektonic animals, such as amphipods, insects, mysids, decapod larvae, and larval juvenile fishes (Myers and Horton 1982; Simenstad et al. 1982; Dawley et al.1986; McDonald et al. 1987). In estuaries, smolts occur in intertidal and pelagic habitats with deep marine-influenced often preferred (Pearce et al. 1982, Dawley et al. 1986; McDonald et al. 1987).

Although pink salmon generally pass directly through the estuary en route to nearshore areas, populations that do reside in estuaries for 1-2 months utilize shallow, protected habitats such as tidal channels and consume a variety of prey items, such as larvae and pupae of various insects, cladocerans, and copepods (Bailey et al. 1975; Hiss 1995).

While in the estuary, lake-rearing yearling sockeye are generally found in faster flowing mid-channel regions and are rarely observed in off-channel areas such as marshes and sloughs. These juvenile fish consume copepods, insects, amphipods, euphausiids, and fish larvae (Simenstad et al. 1982; Levings et al. 1995). In contrast, sea-type and river-type sockeye salmon rear in riverine and estuarine environments. For those "zero-age" sockeye that migrate to the ocean during their first year of life, Birtwell et al. (1987) reports extensive use of estuarine areas of up to 5 months in the Fraser River estuary. During estuarine residence, zero-age sockeye salmon are widely dispersed, with highest concentrations in protected, shallow water habitats with low flow. Common prey during this period include copepods, insects, cladocerans, and oligochaetes (Birtwell et al. 1987; Levings et al. 1995).

There are four general categories of impacts on estuarine ecosystems: enrichment with excessive levels of organic materials, inorganic nutrients, or heat; physical alterations which include hydrologic changes and reclamation; introduction of toxic materials; introduction of exotic species leading to direct changes in species composition and food web dynamics.

Progressive enrichment of estuarine waters with inorganic nutrients, organic matter, or heat leads to changes in the structure and processes of estuarine ecosystems. Nutrient enrichment can lead to excessive algal growth, increased metabolism, and changes in community structure, a condition known as eutrophication. Jaworski (1981) discusses sources of nutrients and scale of eutrophication problems in estuaries. Addition of excessive levels of organic matter to estuarine waters results in bacterial contamination and lowered dissolved oxygen concentrations which then results in concomitant changes in community structure and metabolism. Inorganic nutrients from mineralization of the organic matter can stimulate dense algal blooms and lead to another source of excessive organic matter. The source of high levels of organic matter is normally sewage waste water, but high levels can also result from seafood processing wastes and industrial effluents (Weiss and Wilkes 1974). Impacts from thermal loading include interference with physiological processes, behavioral changes, disease enhancement, and impacts from changing gas solubilities. These impacts may combine to affect entire aquatic systems by changing primary and secondary productivity, community respiration, species composition, biomass, and nutrient dynamics (Hall et al. 1978).

Local physical alterations in estuarine systems include such activities as filling and draining of wetlands, construction of deep navigation channels, bulkheading, and canal dredging through wetlands. Two major types of impacts resulting from these activities are estuarine habitat destruction and hydrologic alteration. For example, canals and deep navigation channels can alter circulation, increase saltwater intrusion, and promote development of anoxic waters in the bottoms of channels. Upstream changes in rivers can also have pronounced effects on estuaries into which they discharge. Construction of dams, diversion of fresh water, and groundwater withdrawals lower the amount of fresh water, nutrients, and suspended input -- all important factors in estuarine productivity (Day et al. 1989).

The measurable consequences of anthropogenic disturbances in the Columbia River estuary have been dramatic since the initial comprehensive surveys and contemporaneous initiation of dredging, diking, shipping, groin and jetty construction, and riverflow diversion between the 1870s and the end of the twentieth century. Thomas (1983) documented a 30% loss (142 square kilometers) of the surface area of the estuary, although some 45 square kilometers have been changed from open water to shallows. Thomas (1983) also reported a 43% loss of tidal marshes and a 76% loss of tidal wetlands. The loss of shallow estuarine areas can shift the estuarine prey composition from benthic crustaceans and terrestrial insects, the preferred food of most salmon smolts, to water-column dwelling zooplankton. These zooplankton are favored by species such as herring, smelt and shad (Sherwood et al. 1990).

Toxic materials include such compounds as pesticides, heavy metals, petroleum products, and exotic by-products of industrial activity near estuaries. Such contaminants can be acutely toxic, or more commonly, they can cause chronic or sublethal effects. Toxins can also bioaccumulate in food chains. The same processes that lead to the trapping of nutrients and thereby to the productivity of the estuary, also lead to the trapping and concentrating of pollutants. Fine sediments not only retain phosphorous and other nutrients, but also petroleum and pesticide residues. Odum (1971) noted that estuarine sediments can concentrate DDT over 100,000 times higher than in the water of the estuary. Such pesticides residues enter the food chain via detritus-eating invertebrates and are further concentrated. The same features of water circulation in the estuary that concentrate nutrients also concentrate pollutants such as mercury and lead, heavy metals from sewage, industrial and pulp mill effluents. Estuarine food chains are extremely complex and sensitive to alterations in the physical and chemical range of stresses. Loss or disruption of one element can have a cascading effect on species presence and productivity.

 

Introduction of exotic species has the potential to change species composition and food web dynamics. See the section on "Introduction and Spread of Nonnative Species" for further detail.

Conservation Measures -- Estuarine Alteration:

Below are the types of measures that can be undertaken by the action agency on a site-specific basis to conserve salmon habitat in areas that have the potential to be affected by estuarine alteration. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat. The following suggested measures are adapted from NMFS (1997), NMFS (1997d), Lockwood (1990), and Meyer, (1997 personal communication).

In addition to the relevant conservation measures listed for "Dredging and Dredged Spoil Disposal", "Irrigation Water Withdrawal, Storage, and Management," "Bank Stabilization, Wastewater/Pollutant Discharge", "Artificial Propagation of Fish and Shellfish", "Offshore Oil and Gas Exploration, Drilling and Transportation", and the "Introduction and Spread of Nonnative Species", the following are suggested to minimize potential adverse effects of estuarine alteration activities.

9. Forestry:

Forest practices can affect salmon habitat. Among the most important effects of forest management on fish habitat in western North America have been changes in the distribution and abundance of large woody debris in streams (Hicks et al. 1991). Timber harvest has reduced the amount and size of large woody debris compared to that in nonharvested areas (Ralph et al. 1994). Large woody debris in streams is a fundamental building block for creating and maintaining salmon habitat. Physical processes associated with debris in streams includes the formation of pools (important to both juvenile and adult salmon) and other important rearing areas, control of sediment and organic matter storage, and modification of water quality. Biological properties of debris-created structures can include blockages to fish migration, protection from predators and high streamflow, and maintenance of organic matter processing sites within the benthic community (Bisson et al. 1987).

Site disturbance and road construction typically increase sediment delivered to streams through mass wasting and surface erosion (Spence et al. 1996). This can elevate the level of fine sediments in spawning gravels and fill substrate interstices that provide habitat for aquatic invertebrates. Fine sediment (usually <0.8 mm diameter ) is detrimental to embryo survival because it reduces substrate permeability (Murphy 1995). The relative magnitude of forest practices on sediment delivery depends on factors such as soil type, topography, climate, vegetation, the aerial extent of the disturbance, the proximity of forestry activities to the stream channel, and the integrity of the riparian zone (Spence et al. 1996). Poor road location, construction, and maintenance, as well as inadequate culverts result in forest roads contributing more sediment to nearby streams than any other forest activity. On a per unit basis, mass wasting events associated with forest roads produce 26-34 times the volume of sediment as undisturbed forests (Furniss et al. 1991).

The removal of riparian canopy reduces shading and increases the amount of solar radiation reaching the streams. The result is higher maximum stream temperatures and increased daily stream temperature fluctuations (Beschta et al. 1987; Beschta et al. 1995). Even small increases in temperature (1-20 C) can result in shifts in the timing of life history events such as spawning and incubation. The cumulative effects of stream temperature changes downstream of logged areas are not well documented.

Fertilizers, herbicides, and insecticides are commonly used in forestry operations to prepare sites for planting, to allow conifers to out compete with other vegetation, and to control diseases and pests. In addition, fire retardants are used to halt the spread of wildfires. These chemicals or their carriers that reach surface waters can be toxic to salmon directly or may alter the primary and secondary production of a stream, influencing the amount and type of food available to salmon (Spence et al. 1996). Risks associated with these compounds depend on the form and application rate of the chemicals, the method of application, whether buffers are maintained, the soil type, weather conditions during and after application, and the persistence of the chemicals in the environment.

Conservation Measures -- Forestry:

Each watershed and each stream reach has a unique set of defining geologic, biological, topographic and other characteristics. An evaluation of effective riparian zone dimensions (for buffering temperature and pollutants, provision of organic debris, and the other elements of healthy EFH) should generate riparian management zones of appropriate width for each stream reach. Mitigation of impacts of forest management activities on salmonid EFH has improved in recent decades. On many federal forests, riparian buffer areas now extend up to 300 feet on fish bearing streams. Land-owners have also become more active in fish restoration and conservation work at the watershed level. Some of this work is being undertaken through watershed groups seeking to restore salmon runs. These watershed groups are composed of the fishing industry, conservation groups, timber industry, state, federal and local government and other stakeholders.

Below are the types of activities that can be undertaken by the action agency on a site-specific basis to conserve salmon habitat to protect and enhance EFH adjacent to forest lands that have the potential to be affected by forestry related activities. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat. The following suggested measures are adapted from Murphy (1995).

10. Grazing:

Livestock grazing represents the second most dominant land use in the Pacific Northwest (after timber production), occupying about 41% of the total land base. An aspect of grazing is the impact it imparts on riparian1/ ecosystems.

1/ Riparian ecosystems can best be defined as "...those assemblages of plant, animal, and aquatic communities whose presence can be either directly or indirectly attributed to factors that are stream-induced or related" (Kauffman 1982).

Riparian areas provide a critical link between aquatic and terrestrial ecosystems. Sustained grazing of these areas can affect substantially fish and aquatic habitats. The riparian zone contributes over 90 % of the plant detritus which supports the entire aquatic biological food chain in upper tributaries (Cummins and Spengler 1974). Even in larger downstream waters, the riparian zone provides over half (54%) of the organic matter ingested by fish (Berner in Kennedy 1977). Management efforts to enhance the riparian zone for one species will generally have positive impacts on many other organisms within this biotype.

The quality and persistence of the riparian zone is a function of its fragility. A large body of research and monitoring indicates that overgrazing by domestic livestock has damaged riparian and stream ecosystems (Armour et al. 1994, Mosely 1997) resulting in decreased production of salmonids (Platts 1991).

Impacts to the riparian zone vary. Livestock grazing can affect the riparian environment by changing, reducing, or eliminating vegetation, and actually eliminating riparian areas through channel widening, channel aggrading, or lowering of the water table (Platts 1991). Soil compaction by trampling can result in a reduction in water infiltration by 40-90% (Rauzi and Hanson 1966, Berwick 1976). Streams modified by improper livestock grazing are also wider and shallower than normal (Duff 1983) leading to pool loss by elevating sediment delivery (MacDonald and Ritland 1989). In addition, removal of riparian vegetation along rangeland streams can result in increased solar radiation and thus increased summer temperatures (Li et al. 1994). Livestock presence in the riparian zone can affect bank stability (Beschta et al. 1993), increase sediment transport rates by increasing both surface erosion and mass wasting (Marcus et al. 1990), and shift vegetative growth to less productive, often exotic plants when Kentucky bluegrass, timothy, and orchard grass replace the native sedges, rye and bunch grasses. Streamside shrubs and trees are also eliminated as the sprouts are browsed by livestock. Regeneration is prevented and the even-aged stands of aspen, willow, cottonwood and associates eventually age, die and disappear (Berwick 1978).

Finally, a major grazing-related historical impact to riparian functions has been (and remains) the clearing of hundreds of thousands of acres of riparian bottoms of willow, mountain maple, cottonwood, and other vegetation which sequestered, pumped, and transpired enormous amounts of water. Ranchers convert meadows to hay pastures of introduced timothy, orchard grass and clover harvested for winter forage throughout the west, often in close functional relationship to salmonid EFH.

Conservation Measures -- Grazing:

Grazing management is key to attaining the benefits which a productive riparian offers livestock while maintaining water quality standards and fully functioning riparian ecosystems (Mosely et al. 1997). Vegetation in riparian areas responds relatively quickly to changes in grazing management and can usually be restored (Platts 1991). Progressive stockmen and land managers have demonstrated there are no insurmountable technological barriers to restoring and protecting the long-term productivity of western riparian areas and adjacent lands (Chancy et al. 1993).

There is great potential for livestock management in the terrestrial and riparian areas of western watersheds to conserve and enhance EFH. Some grazing systems have achieved dramatic successes and others show promise. This is a significant departure from the historically common season-long grazing of summer range riparian zones which resulted in many of the impacts discussed above. Particularly promising are variants of rest-rotation grazing systems. In Idaho, Hayes (1978) found improved forage species composition (i.e., toward pristine deep-rooted perennial climax plants) and a reduction of 65% in bank sloughing with such a system. His data indicate few to no riparian impacts when forage utilization is kept to less than 25%. Bryant (1985 pers. comm.) found that a low/moderate riparian grazing rate promoted more productive, diverse and stable aquatic and riparian systems in the Starkey experimental forest of northeast Oregon. Claire and Storch (in Kauffman 1984) found a rest-rotation system the preferred streamside management if rest is given a pasture for 1 of every 3 years. A four pasture system with summer rest 2 out of 3 years increased riparian browse from 78 to 2,616 plants/ha within two years (Davis 1982). Simulated grazing (clippings) after 1 August had no measurable effects on production or species composition in Wyoming wet meadows (Pond 1961). Late season riparian grazing systems can often increase livestock production, plant vigor and productivity, and minimize wildlife disturbance (Pond 1961, Kauffman 1982). Winter grazing, which considers winter game range use, can effect the same benefits to livestock. Management of stocking rates to reduce damage to wet soils and insure carbohydrate stores for spring growth and vigor is important in these cases (Heady and Child 1994). The above discussion does not address concentrated grazing from dairy cattle which are nowhere near the extent of beef cattle grazing east of the Cascades.

A review of attempts to devise appropriate grazing regimes illustrates the site specific nature of any conservation measure which would presume to be useful. For grazing systems, it has been repeatedly demonstrated that one size does not fit all. The peculiar mix of browse and herbaceous vegetation, warm and cool season grasses, and site factors, dictate local solutions. At each extreme of the grazing spectrum, it has been found that some sites can benefit from continuous grazing at reduced levels while others need rest. An empirically observed rule of thumb which has been supported by numerous studies (including some cited above) is that consumption of annual growth of woody and herbaceous forage on healthy ranges should be held under 50%-60% to provide the nutrients required for initiating new seasonal growth, and prevent range degradation (Hedrick 1950 and Valentine 1970 in Heady and Child 1994).

Below are the types of measures that can be undertaken by the action agency on a site-specific basis to conserve salmon essential fish habitat in rangeland area streams and rivers. Lotic systems are intimately associated with their adjacent riparian zones and can be affected by grazing activity or potential grazing-related impact. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat.

11. Habitat Restoration Projects:

Although intended to help restore salmon habitat or habitat for other organisms, habitat restoration activities can be detrimental to salmon and their habitats. Inadequate, and often absent, analyses of habitat deficiencies and their causes can result in ineffective restoration efforts or habitat injury (Gregory and Bisson 1997, Kauffman et al. 1997, Roper et al. 1997). This should not discourage efforts to restore functional aquatic and riparian ecosystems, but efforts should be part of a watershed or basin conservation plan, carefully monitored and evaluated, and revised accordingly. Efforts should initially identify and eliminate the causes of habitat impairment, and only then consider active restoration techniques to accelerate habitat recovery (Bisson et al. 1997, Lawson 1997).

If restoration efforts are not undertaken with an understanding of the conditions in the watershed, not only may they be unsuccessful, but they may also create additional problems. For example, while stabilizing an eroding bank may improve local water quality, the same treatment may deflect water flow and create erosion elsewhere, thereby decreasing streambank cover, and constricting the natural dynamics of stream channels.

Additionally, habitat restoration activities can be based solely on the needs of an individual species, without consideration of the immediate ecosystem. A single species focus is a concern if the habitat improvement project is designed solely to enhance a particular species, life history stage, or life history pattern. While perhaps being successful in the short term for the limited purpose for which the restoration project was intended, the addition of structure to a channel for specific habitat components in some instances may actually be counterproductive to restoring total ecological functions (Beschta 1997)

Conservation Measures -- Habitat Restoration Projects:

Various documents are available to help those involved in habitat restoration efforts. For example the Environmental Protection Agency has produced a watershed assessment primer (EPA 1994a) and the various impact management techniques to be used for habitat protection and restoration approaches used in the region are described by the Bonneville Power Administration in their watershed management program (BPA 1997). The California salmonid stream habitat restoration manual (CDFG 1994) provides guidance and forms for assessment, monitoring and restoration work. Other habitat restoration guidance documents dealing with everything from in-stream projects, to road maintenance and beaver management have been briefly summarized. Ordering information for the above is provided by "For The Sake of the Salmon" (FSOS 1998). Each state’s fish and wildlife’s habitat division also has information and guidance on habitat restoration activities, including the permits needed, as well as specifications as to when in-stream work is allowed in the various systems.

Below are the types of measures that can be undertaken by the action agency on a site-specific basis to conserve salmon EFH and that have the potential to be affected by habitat restoration activities. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat. The following suggested measures are adapted from Bisson et al. (1997) and Gregory and Bisson (1997).

12. Irrigation Water Withdrawal, Storage and Management:

Water is diverted from lakes, streams, and rivers for irrigation, power generation, industrial use, and municipal use. Additionally, water is withdrawn from the ocean by offshore water intake structures in California. Ocean water may be withdrawn for providing sources of cooling water for coastal power generating stations or as a source of potential drinking water as in the case of desalinization plants.

Potential effects of freshwater system irrigation withdrawals on salmonid EFH include physical diversion and injury to salmon (see below), as well as impediments to migration, changes in sediment and large woody debris transport and storage, altered flow and temperature regimes, and water level fluctuations. In addition, fish and other aquatic organisms may be affected by the reduced dilution of pollutants in rivers and streams where substantial volumes of water are withdrawn. Alterations in physical and chemical attributes in turn affect many biological components of aquatic systems including riparian vegetation as well as composition, abundance, and distribution of macroinvertebrates and fish (Spence et al. 1996). In addition, the volume of fresh water diverted for agriculture can be substantial and can affect both the total volume of water available to salmon as well as the seasonal distribution of flow.

Returned irrigation water to a stream, lake, or estuary project can substantially alter and degrade the habitat (NRC 1989). Generally problems associated with return flows of surface water from irrigation projects include increased water temperature; salinity; pathogens; decreased dissolved oxygen; increased toxicant concentrations from pesticides and fertilizers; and increased sedimentation (NPPC 1986).

Water impoundments can result in raised or lowered summer temperatures, and increases in fall and winter temperatures. Increases in fall and winter temperatures can accelerate embryonic development of salmonid emergence, harming their chances of survival. Low dissolved oxygen can also be a problem in irrigation impoundments that have been drawn down, as is freezing which inhibits light penetration and photosynthesis (Ploskey 1983, Guenther and Hubert 1993). Elevated fall water temperatures from impoundments can also result in disease outbreaks in adult salmon that cause high prespawning mortality (Spence et al. 1996).

Irrigation withdrawals and impoundments also change sediment transport and storage. Siltation and turbidity in streams generally increase as a result of increased irrigation withdrawals because of high sediment loads in return waters (Spence et al. 1996). In some systems, sediments may accumulate in downstream reaches covering spawning gravels and filling in pools that chinook salmon use for rearing (Spence et al. 1996). In other systems, water withdrawals and storage reservoirs can lead to improved water clarity because they trap sediment. This can lead to aggradation of the stream channel as the capacity of the stream to transport sediment is reduced. The settling of gravel sediments behind impoundments and the reduced sediment transport capacity can cause downstream reaches to become sediment starved. This results in loss of high quality spawning areas as substrate becomes dominated by cobble and other large fractions not suitable for spawning (Spence et al. 1996).

Water diversions and impoundments also can change the quantity and timing of streamflow. Changes in flow quantity alters stream velocity which affects the composition and abundance of both insect and fish populations (Spence et al. 1996). Changed flow velocities may also delay downstream migration of salmon smolts and result in salmon mortality (Spence et al. 1996). Low flows can concentrate fish, rendering juveniles more vulnerable to predation (Council 1988).

Water level fluctuations from impoundment releases/storage can de-water eggs, strand juveniles (Council 1988), and, by eliminating aquatic plants along stream bank margins and shorelines decrease fish cover and food supply (Spence et al 1996).

The physical means of withdrawing water may adversely affect salmon. For major irrigation withdrawals, water is either stored in impoundments or diverted directly from the river channel at pumping facilities. Individual irrigators commonly construct smaller "push-up" dams from soil and rock within the stream channel, to divert water into irrigation ditches or to create small storage ponds from which water is pumped. In addition, pumps may be submerged directly into rivers and streams to withdraw water. Effects of these irrigation withdrawals and impoundments on aquatic systems include creating impediments or blockages to migration (for both adults and juveniles), diverting juveniles into irrigation ditches or damage to juveniles as a result of impingement on poorly designed fish exclusion screens (Spence et al. 1996).

Groundwater pumping for irrigation, while providing an alternative to surface water diversion, also can cause a reduction in surface flows, especially summer flows which can be derived from groundwater discharges (Spence et al. 1996).

Conservation Measures -- Irrigation Water Withdrawal, Storage and Management:

Water conservation is one of the most promising sources to meet new and expanding needs for additional water (Gillilan and Brown 1997). For example, Washington state’s Water Resources Management Trust Water Rights Program, started in 1991, provides a means of enhancing instream flows using water saved though conservation. Participants in the instream flow protection processes in the states of Washington, Idaho, Oregon and California include:

California

The state’s most potent instream flow protection is a result of administrative activities of the State Water Resources Control Board, which is required to consider the comments of the state Department of Fish and Game when making decisions about appropriation and transfer permits. Since 1991, individuals have been authorized to change the purpose of existing rights to instream purposes. Private individuals and organizations have also taken advantage of the opportunity to initiate public trust proceedings.

Idaho

Only the Idaho Water Resources Board is allowed to apply to the Department of Water Resources for an instream water right. State statutes allow "the public" to petition the Board to apply for instream flow rights, but the Board has interpreted this language to mean that it may accept petitions only from state agencies. Applications approved by the Department of Water Resources must be submitted to the state legislature for approval.

Oregon

Only the Oregon Water Resources Department may hold instream water rights. The Water Resource Department considers requests from the state Fish and Wildlife, Environmental Quality, and Parks and Recreation agencies. Individuals may acquire existing rights and take responsibility for changing the use to instream purposes in an administrative hearing, but then must turn the right over to the Water Resources Department to be held in trust.

Washington 

The state Department of Ecology establishes minimum flows either at its own initiative or after request from the Department of Fisheries and Wildlife. Because minimum flows are established through administrative rule-making procedures, public notice and hearings are involved. Individuals may donate rights to the sate and specify that they are to be used for instream purposes under the state’s trust water rights program, which is administered by the Department of Ecology.

In 1996, the Bureau of Reclamation released policy guidance on the content of water conservation plans for water districts. Recommended water measures include: 1) water management and accounting designed to measure and account for the water conveyed through the districts distribution system to water users; 2) a water pricing structure that encourages efficiency and improvements by water users; 3) an information and education program for users designed to promote increased efficiency of water use; and 4) a water conservation coordinator responsible for development and implementation of the water conservation plan (Bureau of Reclamation 1996).

Below are the types of measures that can be undertaken by the action agency on a site-specific basis to conserve salmon EFH in areas that have the potential to be affected by irrigation water withdrawal and storage. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat. The following suggested measures are adapted from McCullough and Espinosa Jr. (1996) and OCSRI (1997).

13. Mineral Mining:

The effects of mineral mining on salmon EFH depends on the type, extent, and location of the activities. Minerals are extracted by several methods. Surface mining involves suction dredging, hydraulic mining, panning, sluicing, strip mining and open-pit mining (including heap leach mining). Underground mining utilizes tunnels or shafts to extract minerals by physical or chemical means. Surface mining probably has greater potential to affect aquatic ecosystems, though specific effects will depend on the extraction and processing methods and the degree of disturbance (Spence et al. 1996).

Water pollution by heavy metals and acid is also often associated with mineral mining operations, as ores rich in sulfides are commonly mined for gold, silver, copper, iron, zinc, and lead. When stormwater comes in contact with sulfide ores, sulfuric acid is commonly produced (West et al. 1995). Abandoned pit mines can also cause severe water pollution problems.

Mining activities can result in substantial increased sediment delivery, although this varies with the type of mining. While mining may not be as geographically pervasive as other sediment-producing activities, surface mining typically increases sediment delivery much more per unit of disturbed area than other activities because of the level of disruption of soils, topography, and vegetation. Erosion from surface mining and spoils may be one of the greatest threats to salmonid habitats in the western US (Nelson et al. 1991).

Hydraulic mining for gold from streams, flood plains, and hillslopes occurred historically in California, Oregon, and Washington in areas affecting salmon EFH. Though hydraulic mining is not common today, past activities have left a legacy of altered stream channels, and abandoned sites and tailings piles can continue to cause serious sediment and chemical contamination problems (Spence et al. 1996).

Placer mining for gold and associated suction dredging continues to occur in watersheds supporting salmon. Recreational gold mining with such equipment as pans, motorized or nonmotorized sluice boxes, concentrators, rockerboxes, and dredges can locally disturb streambeds and associated habitat. Additionally, mining activities may involve the withdrawal of water from the stream channel. Commercial mining is likely to involve activities at a larger scale with much disturbance and movement of the channel involved (OWRRI 1995). In some cases, water may be completely diverted from the stream bed while gravel is processed.

Commercial operations may also involve road building, tailings disposal, and the leaching of extraction chemicals, all of which may create serious impacts to salmon EFH. Cyanide, sulfuric acid, arsenic, mercury, heavy metals and reagents associated with such development are a threat to salmonid habitat. Improper or in-water disposal of tailings may cause toxicity to salmon or their prey downstream. On land placement of tailings in unstable or landslide prone areas can cause large quantities of toxic compounds to be released into streams or to contaminate groundwater (NPFMC 1997). Indirectly, the sodium cyanide solution used in heap leach mining is contained in settling ponds from where they might contaminate groundwater and surface waters (Nelson et al. 1991).

Mineral mining can also alter the timing and routing of surface and subsurface flows. Surface mining can increase streamflow and storm runoff as a result of compaction of mine spoils, reduction of vegetated cover, and the loss of organic topsoil, all of which reduce infiltration. Increased flows may result in increased width and depth of the channel.

Mining and placement of gravel spoils in riparian areas can cause the loss of riparian vegetation and changes in heat exchange, leading to higher summer temperatures and lower winter stream temperatures (Spence et al. 1996). Bank instability can also lead to altered width-to-depth ratios, which further influences temperature (Spence et al. 1996).

Conservation Measures -- Mineral Mining:

State and federal law (i.e., the Clean Water and Surface Mining Control and Reclamation Acts) contain provisions for regulating mining discharges. State and local governments are taking an increasingly active role in controlling irresponsible mining operations (Nelson et al. 1991) and most western states require operators to draw up a mining plan that details potential environmental damage from that operation, and reclamation and performance bonds must be posted (Nelson et al. 1991). A challenge still lies in the reclamation of the thousands of abandoned sites that have or may potentially impact salmon EFH.

Below are the types of measures that can be undertaken by the action agency on a site-specific basis to conserve salmon EFH in areas that have the potential to be affected by mining related activities. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat. The following suggested measures are adapted from recommendations in Spence et al. (1996), NMFS (1996) and WDFW (1998).

14. Introduction/Spread of Nonnative Species:

Introduction of nonnative plant and animal species may be either deliberate (to enhance sport-fishing or control aquatic weeds, for example) or accidental without thought to the consequences (e.g., the dumping of live bait-fish and the seaweeds in which they are packed, aquaculture escapees, the pumping of bilge or ballast water, or releases from aquariums by individuals). Although the impacts are poorly known, the introduction or spread of nonnative species into areas of salmon EFH can potentially alter habitat process and function. Introduced fish can dominate or displace native fish through various mechanisms including competition, predation, inhibition of reproduction, environmental modification, transfer of new parasites or diseases and hybridization (Spence et al. 1996).

In the Columbia Basin, introduced predator species including walleye, channel catfish, and small mouth bass have high predation rates on outmigrating salmon smolts. Boyd (1994) reports that the presence of striped bass in a river system near California’s San Francisco Bay region resulted in estimated losses of 11% to 28% of native run of fall chinook . White bass and northern pike introduced into the inland delta of the Sacramento and San Joaquin rivers prey on salmon and other species (Cohen 1997). In Oregon’s coastal lakes and reservoirs, introduced fish species such as striped bass, largemouth bass, small mouth bass, crappie, bullheads and yellow perch have become established with obvious predation impacts in some basins and negligible impacts in others. For example, nonendemic Umpqua squawfish are voracious predators of juvenile salmonids in Oregon’s Rogue River basin (Satterwaithe 1998, pers. comm.) and the Coos and Umpqua estuaries contain striped bass that prey on salmonids (OSCRI 1997). Introduced grass carp and common carp can destroy beds of aquatic plants which results in concomitant reductions in cover for juvenile fishes, destruction of substrates supporting diverse invertebrate food chain assemblages, and increases in turbidity (Spence et al. 1996).

Many typical warmwater species from other regions, such as small mouth bass, carp, and catfish have been introduced as exotics to the Snake River basin. Displacement of salmonids and other cold water species by native coolwater species (e.g., redside shiners) or by the exotic warmwater species results in a reduced total usable habitat area for spawning and rearing and, thereby a diminished production capability for salmon (McCullough et al. 1996).

The introduction of organisms other than fish is also of great concern in estuarine environments. The food webs of San Francisco Bay have been dramatically altered by this invasion, more recently by the arrival of an Asian clam which has multiplied to such abundance that it can filter all the water over a significant portion of the bay in less than a day, removing bacteria, phytoplankton, and zooplankton in the process and leaving little behind for other organisms (RAC 1997).

Introduced plants can also have serious detrimental effects on salmon habitat. The exotic aquatic plant, egeria (Egeria densa) is known to harm coho rearing in coastal lakes (OCSRI 1997). The spread in estuaries of various species of cordgrass (Spartina spp.) and another grass, the common reed (Phragmites australis), are of concern. Spartina spp. may affect salmon habitat in a number of ways, many of which appear to be detrimental to salmon and their prey. Spartina forms dense uniform stands in the upper intertidal area, traps sediment and raises the elevation of the mudflat. The macroinvertebrate population in areas dominated by Spartina alterniflora is somewhat different than that in mudflat areas. Nonnative plant invasions may decrease food for some species such as chum salmon that feed on the mudflats, while it may increase resources for chinook salmon that feed on invertebrates in the water column or on the surface, though the interactions are complicated and are still being studied (Luiting et al. 1997).

Other effects from Spartina invasion (as well as from Phragmites) results from the meadows being a good filter of nutrients and sediment washing off the land. While this may be beneficial in terms of reducing pollution, it can also have negative effects by raising the elevation of the high intertidal area and sequestering nutrients from the estuarine system.

Efforts to control Spartina and other exotics may cause additional affects to salmon and their habitat. Long term impacts of either the use of mechanical mowing measures or of the use of herbicides (e.g., Rodeo®) and various surfactants have not been well studied. Concerns exist on both the acute and sublethal toxicity to nontarget species and the potential for bioaccumulation. These chemicals are known to adsorb to sediments under certain conditions and some of the surfactants are known to be estrogen disrupters in fish (Felsot 1997). The use of biological control agents is also under study.

Many of the region’s riparian habitats have also been extensively altered by invasive species (e.g., blackberries, reed canary grass, and scotch broom), deterring the establishment of native species, and altering the habitat (e.g., shading, stream bank stability) and the nutrient cycling characteristics of the area. The effects of these changes are not fully known.

Conservation Measures -- Introduction/Spread of Non-Native Species:

Watershed management strategies for enhancement and conservation of salmon EFH in many instances will include restoration of water flows and riparian areas, as well as other habitat conditions. These measures should discourage nonnative species from establishing or expanding their territories (i.e., colder water will favor salmonids over centrarchids).

Below are the types of measures that can be undertaken by the action agency on a site-specific basis to conserve salmon EFH in areas, that have the potential to be affected by the introduction of non-native or non-endemic species. Not all of these suggested measures are necessarily applicable to any one project or activity that may adversely affect salmon EFH. More specific or different measures based on the best and most current scientific information may be developed prior to, or during the EFH consultation process, and communicated to the appropriate agency. The options listed below represent a short menu of general types of conservation actions that can contribute to the restoration and maintenance of properly functioning salmon habitat. The following suggested measures are adapted from Cohen (1997).