Long Range Plan for the Klamath River Basin Conservation Area Fishery Restoration Program
Part 1 of

CHAPTER 3: HABITAT RESTORATION

CHAPTER 3: HABITAT RESTORATION

* The ability of instream work to correct fish habitat degradation is limited, unless the underlying watershed problems that cause degradation are also addressed.

* Must detailed habitat analysis necessarily precede investments in habitat restoration?

* Who should pay for the watershed restoration, streamflow augmentation and erosion control efforts necessary to protect and restore fish habitat?

* The need to work with ranchers to restore riparian zones to prevent erosion from destroying pasture land and to improve fish habitat.

* The need to improve streamflows, particularly in the Shasta and Scott river valleys, in ways that do not disrupt ranching.

* The need to gain a better understanding of the Klamath Basin through the use of aerial photography, Landsat imagery and other available technical resources.

INTRODUCTION

This chapter describes the methods that have been used in attempts to restore the fisheries habitat of the Klamath River Basin and the degree of success such attempts have enjoyed. Suggestions regarding appropriate means to approach habitat restoration during the balance of the Klamath River Basin Fisheries Restoration Program are made.

We must quit looking at just a pool, a riffle, or even a reach, but address the problem as it fits into a complete watershed. How often have we visited a good looking K-dam, stream deflector, or rock crib to enhance a small reach, only to look around the watershed and see it crumbling down upon us.

W.S. Platts

Bill Platts made these remarks at a 1984 habitat management workshop (Hassler 1984) that would prove to be a turning point in the use of instream structures for improving degraded fish habitat. Instream structures enjoyed a surge in popularity in the 1930's, largely for erosion control in the Midwest (Silcox 1936, Tarzwell 1938). As early as 1934, the California Department of Fish and Game (Burghduff 1934) acknowledged that stream improvement involving "retardation of stream flow by the construction of weirs and erosion dams ... do not fit existing conditions in most of our western streams, which are precipitous, rock-bound, and fall thousands of feet in a score of miles."

Despite the recognition that these instream structures did not work for most of California's streams, the Civilian Conservation Corps built them throughout the Great Depression. After evaluating these efforts, Calhoun (1966) concluded that attempts to treat California streams with instream structures had "no instances of reasonable success."

Taft and Shapovalov (1935) surveyed many of the streams of the Klamath Basin and found that, for the most part, they provided "fine pools for shelter, trees and brush for shade and to furnish terrestrial food, and many riffles to provide abundant food and spawning areas. Thus they do not seem to call for 'stream improvement' in the accepted meaning of the term." Noted exceptions were several diversion dams without ladders and "hanging" road culverts which blocked fish migration. While the stream habitat conditions found by Taft and Shapovalov may have been much different than those of today, theirs is still a valid prescription for improvement: "From the viewpoint of fish life, the most important improvement that could be effected in streams would be the general restoration to natural conditions."

Many of the stream channels of the Klamath River Basin are so disturbed today their complete restoration could well take longer than the life of the Restoration Program. Every increment of well planned habitat improvement will help, therefore, in the rebuilding of the region's fish populations. Moreover, while early restoration efforts suffered from a poor understanding of the factors that limit salmonid fish production, including inadequate knowledge of stream dynamics (Everest and Sedell 1984), renewed public interest in stream restoration has fostered a substantial increase in our abilities.

Bisson et al. (1981) and, more recently, McCain et al. (in press) have developed systems for classifying the types of fish habitat in streams. As habitat use by salmonids is noted, fisheries biologists have been able to focus more closely on the factors which limit the production of salmon and steelhead. Although habitat typing by itself does not provide a complete understanding of limiting factors, further work by Reeves et al. (1989) has provided a key which can be used to identify stream production bottlenecks for juvenile coho salmon. Hankin and Reeves (1988) have developed methods for estimating basin-wide salmonid populations in tributaries, based on the number of fish which use different habitats and the number of habitat units found in the stream.

While fisheries science has been exploring the habitat elements that limit salmon and steelhead production, the use of instream structures to mimic these elements has been widely tested throughout the Pacific Northwest (Anderson 1988). The compatibility of different treatments is now checked against stream gradient, streambed stability, height of flood flows and other critical data to assure that the structure will remain in place, at least during moderate storm events, and will function as intended. Studies of undisturbed stream systems have improved the design criteria for habitat restoration projects significantly (Sedell and Luchessa 1981).

Some of the best habitat restoration information has come from the study of geomorphology and hydrology. While fisheries managers have long been able to recognize degraded fish habitat, geologic information now provides insight into the root causes of that degradation (Hagans et al. 1986). In addition, knowledge of geology can help to determine the stage of recovery of a stream (Lisle 1981), whether an oversupply of sediment is likely to continue, and whether attempts to structurally manipulate a stream are prudent (Lisle and Overton 1988). Prioritizing erosion prevention in this way can help reduce the amount of sediment likely to reach the stream (Weaver and Hagans 1990). As watersheds are stabilized, the recovery of stream channels will be accelerated.

It has been a challenging task to evaluate instream structures to determine their cost-effectiveness (Everest and Sedell 1984). While the costs of projects are easy to determine, the number of fish which they produce can be difficult to establish (Fontaine 1988). Arriving at a value for the fish produced by a project can also be a complex process (Meyer 1980).

Methods of improving or restoring fish habitat, in addition to those involving channel and bank stabilization, include the removal of barriers to migration, screening stream diversions to reduce the loss of both juvenile and adult fish, increasing stream flows, replacing gravel, creating spawning or rearing channels below dams, and restoring riparian vegetation.

Public interest and support for salmon, steelhead, and trout restoration have grown rapidly in the past decade. Community groups in California have become an integral part of restoration, both for fund-raising and for carrying out projects. While volunteer effort lends the obvious advantage of enabling projects at low cost, it serves even more importantly to create a grass-roots, or community-level, commitment to fish conservation. Many of the state's restoration groups are associated with the California Salmon, Steelhead and Trout Restoration Federation, which holds annual meetings to share technical information and the restoration spirit. The Oregon Salmon and Trout Enhancement Program (STEP) has also been highly successful as a catalyst for involving the public in fish restoration. STEP projects have included instream structures, hatch boxes, rearing ponds, and education programs.

Although the art of fisheries restoration has advanced considerably in recent years, some still question whether structural manipulation of anadromous fish habitat is an effective strategy for increasing production of these fish (Nawa 1987). It is generally understood that instream structures are no substitute for good watershed stewardship, including the protection of productive fish habitat (Anderson 1988, Everest and Sedell 1984, Reeves and Roelofs 1982). Improving fish habitat through watershed restoration takes years, while instream structures can offer habitat improvement much quicker. In an ideal situation, structures would be used to accelerate habitat recovery after watershed stabilization is well underway. The Task Force may be required, however, to use instream structures for immediate habitat improvements to benefit those fish stocks identified in Chapter 4 as priorities for recovery.

HABITAT RESTORATION METHODS

Fisheries habitat improvements can involve four general areas: instream work, riparian area restoration, streamflow improvement and watershed stabilization.

Improving Access to Spawning Areas

Barriers to fish migration have long been identified as impediments to anadromous fish production and fishways have been constructed for 200 years or more. The sophistication of fish passage facilities benefitted from research associated with construction of dams on the Columbia and Snake rivers (Savage 1986). Fish ladders that bypass dams can be a series of simple jump pools or elaborate systems involving elevators (Bell 1973). Passage over natural barriers or short, steep impediments like culverts, use vertical slots with baffles to slow the flow and allow upstream migration (Clay 1961). The most common vertical slot type fishways are the Alaska steep pass and the Denil ladder (Ziemer 1962). A common objective of all fishway designs is a good attraction flow and an easy entrance for the fish.

Figure 3-1 -- Before installation of an Alaska steep pass, this culvert was a barrier, at low flows, to salmon and steelhead trying to reach their spawning grounds.

Heavy equipment has been used on mid-Klamath tributaries to modify sediment plugs near stream mouths that create fish migration barriers (J. West personal communication). Other barrier modifications have included log jam removal and blasting of rock barriers. Recent work by Sedell et al. (1988) indicates that, in our haste to provide fish passage, we may have removed large woody material that provided essential habitat elements.

Fish Screens Reduce the Loss of Juveniles

Fish screens are used to prevent juvenile salmonids from being drawn into agricultural diversions. These devices range from huge drum screens that block passage into major California irrigation canals to simpler devices to keep downstream migrants out of small ditches leading to pastures. Recent designs provide for the screens to be self-cleaning to prevent them from becoming clogged with algae or floating debris.

Figure 3-2 -- Fish screens, such as this one along Shackleford Creek, a Scott River tributary, save thousands of young salmonids from being diverted into the fields.

Improving Fish Habitat With Instream Structures

Improvement of spawning conditions has been a major focus of instream habitat efforts. Gabions, log weirs, boulder weirs and other structures have been used successfully to trap spawning gravels (House 1984). Rearing habitat can be created for juvenile salmonids by providing cover and causing pools to form by the use of drop structures or by placing boulders, logs, or large root wads to cause scouring (Anderson 1988). Pools can also be created by blasting. These techniques are typically used in streams that have suffered degradation and that lack habitat complexity.

Streamflow Improvements Add Spawning and Rearing Habitat

Both spawning and rearing habitat can be increased by increasing flows below dams or diversions. Iron Gate Dam was constructed to reduce fluctuations in flows caused by upstream hydroelectric operations. The fluctuations caused stranding of adult salmon and steelhead and heavy mortality of juveniles. Claire Engle and Lewiston Dams on the Trinity River were completed in 1964 and divert over 80% of the river's flow into the Central Valley for agricultural use. Flows in the Trinity River have been improved over pre-1980 levels in order to study their benefit to fisheries resources (Hampton 1988). The U.S. Forest Service has worked to retain instream flows in order to maintain river channels through National Forest Lands in Colorado (Randolph 1990). Channel maintenance flows have emerged as an issue on the Trinity River (Bob Franklin personal communication). The periodic relicensing of major dams by the Federal Energy Regulatory Commission provides the opportunity to negotiate improvements in flows for fish (Echiverra 1989). Opportunities for increasing streamflows for fish through water conservation measures are being explored in Oregon, California, and Montana (see Chapter 2).

Special Restoration Techniques Appropriate Below Dams

To the extent that dams stabilize flows in the stream reaches below them, they make structural treatments in those reaches more practical. Smaller gravels and cobbles suitable for spawning are washed downstream below dams, however, and the recruitment of replacement gravel is prevented by the dams. Severe loss of the quality and quantity of pre-dam spawning habitat frequently occurs. To counteract such loss, new spawning gravels have been trucked to stream reaches below dams. The absence of flushing flows cause gravels to become so impacted with silt that they become unsuitable for spawning. Heavy equipment has been used extensively to loosen silted spawning gravels in Washington state (Savage 1986). Pools have been dredged below Grass Valley Creek on the Trinity River to provide holding areas for adult spring chinook (USFWS in press).

Side channels can be added below dams for spawning and rearing as the dams make high flows less likely. The concentrations of fish returning to hatcheries built below dams uses the stream habitat improvements made at these sites.

Restoring Riparian Areas Can Yield Big Dividends

The vegetated areas next to streams provide bank stability, cover for fish, habitat for birds and animals, shade to keep water temperatures cool, terrestrial insects for fish to eat, leaf litter which fuels the aquatic food chain, and recruitment of logs which provide instream structure. Riparian vegetation also traps fine sediment and organic matter during high flows, thereby helping to build banks (Platts 1984a). Elmore (1988) has found that a healthy riparian zone acts as a conduit for recharging ground water.

Where livestock grazing has decreased riparian vegetation, streamside areas can be fenced and grasses, shrubs and trees replanted. The stabilization of streambanks with riprap, gabions, or log revetments can prevent bank erosion but may not provide optimal fish habitat unless done in conjunction with riparian planting. Riparian zones in forested streams can also be replanted but if sediment supply remains high, channel instability can make it difficult for trees and shrubs to become reestablished. Natural regrowth of conifers can take over one hundred years after severe flooding or logging in stream side areas (Lisle 1981).

Watershed Rehabilitation: Helping Nature Restore Fish Habitat

Watershed restoration to benefit fish resources would begin with an inventory and evaluation of sediment sources, the changes in sediment supply likely to result from storms or changes in land use, and the relative magnitude of the different sediment sources (Weaver and Hagans 1990). From this basic information a sediment budget can be formulated and priorities for treatment established. Treatments may include attempts to stabilize a slide by revegetating it, armoring the toe of a streamside landslide, putting roads "to bed," removing or enlarging culverts, outsloping roads or installing waterbars, dewatering slides, mulching and planting bare slopes, and a host of similar measures (Mattole Restoration Council 1989).

Figure 3-3 -- Riparian restoration improves fish habitat dramatically.

Top: Stream before treatment. Middle: After installation of boulder weirs, at a higher flow. Bottom: Streamside replanting beginning to mature.

While erosion prevention work may seem costly, it is much less expensive than the removal of sediment from stream channels after it has left the hillsides. The investment in instream structures and riparian restoration efforts may be ineffective if a high rate of sediment continues due to erosion in upslope areas. Natural processes created fish habitat, and if watersheds are restored and protected by improved land use practices, good fish habitat will return. Watershed measures may take longer to dramatically alter specific sites within streams, but once implemented their benefits are long-lasting and will enable the stream to restore itself over its entire length, not just in treated reaches.

CHOOSING APPROPRIATE FISHERIES RESTORATION STRATEGIES

Before effective action can be taken to restore fish populations, project planners should have enough information to determine which factors are limiting the production of the species to be restored (Everest and Sedell 1984). Only then can they determine accurately which treatments to use. Some limiting factors may be obvious, such as diversion of the entire flow of a stream during spawning or outmigration seasons. If substantial numbers of juvenile salmonids are being lost to irrigation, then installing fish screens is clearly logical, but when considering the use of instream structures to increase specific habitat elements, a much closer look at limiting factors is needed. Habitat needs should be determined on a basin-wide, or subbasin wide, scope and should include both biological and physical habitat assessments (Reeves 1988).

Using Fish Abundance To Determine Restoration Needs

The presence or absence of anadromous fish above a perceived barrier obviously can indicate whether barrier modification or construction of a fish pass is needed. Using fish populations to assess the need for habitat restoration measures can as easily be misleading, however. Low fish numbers can result from harvest or poor access, in low water years, of spawning migrations. For this reason, it is desirable to have estimates of fish numbers for several years. Spawner counts, electrofishing, and direct observation are three established means of estimating fish numbers.

The number of salmon spawners can be estimated by counting carcasses or salmon redds. As carcasses are counted they are marked with a tag or cut in half. Subsequent counts use the ratio of marked to unmarked carcasses to estimate the total number of spawners. Steelhead are much more wary than salmon while spawning, do not always die after reproduction and cannot, therefore, be counted in this way.

Electrofishing is also used to estimate fish numbers. The stream reach is blocked with nets and the fish in the area are stunned with electricity and counted. Several passes may be made to collect as many of the fish within the section as possible, and statistical methods are used then to determine the total number of fish present (Platts et al. 1983). In a small or medium sized stream, electrofishing can give a very accurate assessment of fish populations in the area sampled. Extrapolating these results to estimate basin population totals can lead to significant errors (Everest et al. 1986). Hankin (1986) asserted that errors in population estimates for basins resulted more from expanding data from small stream segments than from the accuracy of the counts within the segments themselves. He suggested conducting population estimates by habitat units, and not on arbitrary lengths of stream, can help reduce this error.

When water clarity is good and stream depth is sufficient, direct observation by divers is the best method for determining populations of salmonids over a basin-wide area (Hankin and Reeves 1988). The numbers of fish are related to the habitat types in which they are counted. Expansions are based on the total number and area of habitat types in the basin. Visual estimation is much quicker than electroshocking, so more stream area can be counted by direct observation and the errors associated with extrapolation can be reduced. To check the validity of these counts or to estimate the degree of bias, a subsample of habitat units where fish were counted by direct observation can be electroshocked and the numbers compared.

Figure 3-4 -- Divers with masks and snorkels estimate fish populations by direct observation.

Physical Factors Determine Restoration Techniques

If a stream appears in need of rehabilitation, the first level of assessment should include an historical search to determine when changes may have occurred, what caused the changes (e.g., logging followed by a large flood event), and whether the watershed in question still contains major sources of sediment. The use of aerial photos is a quick and cost-efficient way to study changes over time (Grant 1988) and to assess current watershed conditions (Weaver and Hagans 1990). If significant sediment sources still exist in a basin, then instream structures are not a prudent investment because it is likely they will soon be buried or rendered dysfunctional (Lisle and Overton 1988). Erosion prevention measures and, where necessary, changes in land use practices should be pursued first.

If the watershed under study no longer has significant erosion problems, the next step would be an attempt to determine the current stage of stream channel recovery (Lisle 1981). If the streambed has become aggraded it may be unstable and untreatable until it approaches its former elevation (Lisle and Overton 1988).

Rosgen's channel typing (1985) system can be used in this stage of analysis to help determine whether particular reaches are compatible with particular treatments. Lisle and Overton (1988) suggest that structures to retain spawning gravel should not be placed in stream reaches having a gradient of less than 0.25 percent nor greater than 1 percent. Any stream having a gradient greater than 2 percent (Lisle and Overton 1988) or 2.5 percent (Anderson 1988) is generally unsuitable for instream structures due to the force of water during high flows. All instream work should take into account the hydraulic forces which occur at flood stages and the expected interval at which potentially destructive flows might occur.

After the larger questions of whether the watershed and stream bed are suited to structural treatment, an in-depth fish habitat survey can be conducted (Bisson et al. 1981 and McCain et al in press). Hampton (1989) suggests that, as a first step, the freshwater life stages of each target species, and their respective habitat requirements, should be understood. In this way, the relative abundance of habitats may indicate what is limiting the production of the species of interest (Hampton 1988). Knowledge of the adjacent streams would be helpful since preferred habitats may be lacking altogether. Habitat typing is generally conducted at low summer flows, leading to the frequent conclusion that rearing habitat at these flows is the limiting factor. Increasing the amount of such habitat might not increase smolts production, however, if a more important problem is winter survival (Mason 1976, Hampton 1988). Thus, even where restoration projects are undertaken after habitat typing and limiting factor analysis, such projects should be evaluated to see if they were, in fact, the solution to low fish abundance.

Other important questions regarding habitat that should be addressed before structural treatments are pursued are those of water quality and quantity. It makes little sense to structurally treat a stream where water quality will not support fish life. Water can be tested for temperature, dissolved oxygen, or pollutants (American Public Health Assoc. 1987).

THE EFFECTIVENESS OF PREVIOUS HABITAT RESTORATION EFFORTS

A Task Force compilation of projects undertaken to improve fish conditions in the Klamath River Basin, including the Trinity River, (USFWS 1988b) indicates that $7.8 million has been spent on such efforts since 1958. Funds for these projects have come from the U.S. Soil Conservation Service, California Department of Fish and Game, U.S. Forest Service, U.S. Bureau of Indian Affairs, Hoopa Valley Tribal Council, California Conservation Corps, Pacific Power and Light Co. and the U.S. Bureau of Reclamation.

Since 1984 there has been a significant increase in fisheries restoration activity in the Klamath Basin. Substantial amounts of funds for fish restoration have been provided directly by legislation, as well as by voter initiatives. The 1984 Trinity River Restoration Program (P.L. 98-541) and the 1986 Klamath River Basin Fisheries Restoration Act (P.L. 99-552) have specifically committed the U.S. Department of Interior to fisheries restoration

efforts in the Klamath-Trinity basins. Congress has expanded the U.S. Forest Service's role in fisheries conservation in recent years (P.L. 93-452, P.L. 94-588), as well.

The Task Force's planning consultants, William M. Kier Associates, inspected nearly two-thirds of the projects listed in the 1988 compilation during the summer and fall of 1989. Their observations, which are summarized in Appendix C, concerned only the physical integrity of structures and their apparent success in creating their intended stream conditions. There was not sufficient opportunity to determine the success of the structures in producing fish, or their cost-effectiveness. The following discussion draws heavily on the 1989 field review, although some examples from other areas are discussed as well.

Success In Improving Access For Migrating Fish

The Klamath Basin projects to provide fish access past migration barriers have, for the most part, been successful. Many projects conducted by the California Conservation Corps (CCC) in the lower basin have involved modifying log jams to allow migration. Unlike earlier efforts that totally removed jammed logs, the CCC now leaves much of the material in the channel to act as cover or to form natural structures. Hewitt ramps were installed on Ah Pah Creek, and appear successful in passing fish. A baffle installed by the Redwood Community Action Agency on a Richardson Creek culvert eliminated what was a velocity barrier to coho and chinook salmon.

On Tarup Creek, the CCC improved fish passage by blasting a bedrock waterfall believed to block chinook salmon migration. Similar methods were used to open up five miles of Dillon Creek to both salmon and steelhead. Low cost projects that open areas in a highly productive streams like Dillon Creek are excellent investments in restoration. Opening Bluff Creek to salmon and steelhead, after access was blocked by the 1964 flood, represents a major success in fisheries restoration. Blasting opened three miles of habitat on Clear Creek and log jam removal on its South Fork opened an additional one and a half miles of habitat to summer steelhead, as well as other runs of salmon and steelhead (D. Maria personal communication).

Several successful barrier modifications in the Salmon River Basin have been carried out, including projects on Black Bear Creek, St. Claire Creek, and Knownothing Creek. A rock fall which blocked chinook salmon migration in the main stem of the Salmon River was altered. Chinook and coho salmon numbers doubled in Knownothing Creek after treatment. A step and pool ladder was constructed on Nordheimer Creek, a tributary to the Salmon River. The ladder, located one and a half miles above the mouth of the creek, helps fish travel over a 14-foot-high bedrock falls and opened up three miles of additional habitat to anadromous fish. A large number of adult steelhead climbed the ladder in 1988, the first year it was available (D. Maria, personal communication). Barrier modification on Kelly Gulch in the Salmon River failed to assist chinook salmon passage, but improved access for migrating steelhead.

Additional habitat in Indian Creek has been made available by the removal of several obstructions to migration. Four ladders have been constructed on the Shasta River and they function. Access to Independence Creek was blocked until the mouth of the stream was altered. Steelhead are now seen entering this system in the fall before major winter flows (J. West personal communication). A fish pass on Coon Creek works at some flows, but requires ongoing maintenance.

Fish Screens, Rescue Efforts Save Juvenile Salmon and Steelhead

The California Department of Fish and Game's Yreka fisheries staff devotes a considerable amount of effort to keeping juvenile salmonids out of irrigation diversions. The Scott and Shasta rivers and their tributaries require much of this work, but several small mainstem Klamath tributaries, including Bogus Creek, Cottonwood Creek, Little Bogus Creek, Cold Creek, and Dry Creek are also important fish screen and rescue work areas.

Screens are installed at ditch intakes to prevent the juvenile fish migrating downstream from being drawn into the fields. Downstream migrant traps are placed above dewatered stream segments. Fish rescue operations at screens and traps save about 450,000 juvenile salmonids a year. Huntington (1988) found that fish screening and rescue efforts were very cost effective. He estimated a cost-benefit ratio of 3.1/1 for screening operations. Problems at screens can arise from lack of maintenance, and screens are sometimes removed or not installed when needed (D. Sumner personal communication). An additional worker has been added to Fish and Game's Yreka office to help keep up with the increasing screen operation and maintenance needs (R. Dotson personal communication).

New screens are planned for Bogus and Cold creeks which will complete the screening of stream diversions in the entire Bogus Creek watershed. Four additional screens are needed in the Kidder Creek drainage and will be installed over the next two years. Another priority is a main diversion ditch in the West Fork of the Scott River. Screen priorities are based on the potential loss of fish at each diversion site. There are currently 56 screens in the area served by the Fish and Game's Yreka staff (R. Dotson personal communication).

Mixed Results From Instream Habitat Structures

Instream structures to increase spawning and rearing habitat for juvenile salmonids generally use materials available at the site, typically logs and boulders. While the majority of the structures surveyed in 1989 appeared to be functioning as intended, many were partially or totally disabled.