Youngs Bay Population

LC Coho Tributary Habitat Information – Youngs Bay Population

Compiled by NMFS for ODFW Recovery Planning Expert Panel Process – 12/2005

Lower Columbia Coho Evolutionarily Significant Unit

YoungsBay Population

Table of ContentsPage

Geographical Overview 2

W/LC TRT Population Assessment 2

Habitat Complexity 3

Fish Passage 6

Riparian Condition 7

Water Quality 9

Water Quantity 14

Substrate 16

Hatchery 17

Works Cited 18
Geographical Overview

The YoungsBay watershed is a fifth field watershed located in the northwest corner of

ClatsopCounty. YoungsBay is an arm of the Columbia River estuary. It is

approximately two miles wide at its confluence with the Columbia River estuary and is situated between the cities of Astoria and Warrenton. The Lewis & ClarkRiver, YoungsRiver, KlaskanineRiver, and WallooskeeRiver flow into YoungsBay, draining approximately 184 sq. mi. of land. The primary economic land use in the YoungsBay watershed is timber harvest, with some agriculture in the lowlands (Bischoff, et al. 2000).

W/LC TRTYoungsBay Population Assessment

Details of the W/LC TRT evaluation method are described in the Interim Report on Viability Criteria for Willamette and Lower Columbia Basin Pacific Salmonids (2003). This document is available at the following website:

Following is a brief summary of the evaluation method. For the evaluation, populations were ranked for absolute extinction risk on a scale of 0 to4. The extinction risks associated with each value on the 0–4 scale are summarized below.

It isimportant to note that the persistence categories (0–4) do not represent a linear scale. Forexample, the persistence probability associated with category 0 has a much greater range (0–40%) than category 4 (> 99%). Extinction risk is the complement of persistence probability (i.e.,extinction risk = 1 – persistence probability). To estimate population extinction risk, four key attributes were evaluated: abundanceand productivity, diversity, spatial structure, and habitat. A fifth population attribute, JOM growth rate, is part of the W/LCTRT viability criteria, but did not havemuch impact on the population evaluationsdue to lack of data. The four main population attributes were evaluated on the same 0–4 risk scale. Toobtain the overall population score, individual population attribute scores were integrated using asimple weighted mean; the abundance and productivity scores were weighted at twice the otherscores (McElhany, et al. 2004).

The W/LC TRT population status evaluations were based on a set of data atlases compiled by the NorthwestFisheriesScienceCenter in 2003.

Table 1.TRT Viability Assessment (McElhany, et al. 2004).

Weighted average: 0.86

Productivity and abundance: TRT comments focused on the declining trend in abundance, the 91% hatchery contribution to escapement, and the very low overall abundance (especially during the 1990s).

JOM: Not rated.

Diversity: Large-scale hatchery releases and the relatively poor contribution of natural origin recruits to escapement are the major negative factors.

Habitat: Poor habitat conditions exist throughout YoungsBay tributaries. Development and timber harvest are sources of degradation.

Spatial structure: No major blockages were identified (although there was some discussion about the hatchery weir on the Klaskanine as a potential impediment). Numerous small blockages (tide gates, culverts) may influence access to smaller tributaries and side channels. Patches of poor habitat could also affect the distribution of coho salmon (McElhany, et al. 2004).

Habitat Complexity

By far, the most significant alteration to the YoungsBay watershed (lower Lewis and Clark and Walluski rivers, the mouth of YoungsBay, and the east side of YoungsBay) has been from diking for flood protection (Bischoff et al. 2000). Extensive diking occurred between 1917 and 1939, disconnecting the floodplain from the stream. Bischoff et al. (2000) also noted that YoungsBay has a history of dredging to maintain navigability for the Port of Astoria. The lower 4.5 miles of the Lewis and ClarkRiver were dredged in 1973 and the dredge spoils were placed on diked areas along the river. Based on their Qualitative Habitat Assessment (QHA), LCEP and LCFRB (2004) gave the highest ranking to channel stability (defined as the condition of the channel in regard to bed scour and artificial confinement[1]) and habitat diversity (diversity and complexity of channel including the amount of large woody debris and multiple channels) in the lower Youngs River (i.e. up to the falls at RM 8) for protection and restoration.

Table 2.Riparian and Large Woody Debris Conditions in YoungsBay Watershed (Bischoff, et al. 2000).

YoungsBay has a long history of dredging to maintain navigability for the Port of Astoria. Historically, the Lewis and ClarkRiver has been dredged to maintain navigability, including dredging in 1956 and 1962. The history of dredging is too extensive to list here. However, YoungsBay has been historically altered to maintain channel navigability which has led to losses in aquatic habitats.

Table 3.Stream morphology and substrate in the YoungsBay watershed

(Bischoff, et al. 2000).

Table 4.Summary of Life Stages and VSP Parameters Affected.

Life
Stages
Affected / Egg to Parr / Parr to Smolt / Smolt to Adult
Incubation / Early Rearing / Summer Rearing / Winter Rearing / Downstream Migration / Estuary Rearing / Ocean Residence / Upstream Migration / Spawning
X / X / X / X / X / X / X
VSP Parameters Affected / Abundance / Productivity / Diversity / Spatial Structure
X / X / X / X

Fish Passage

Fish populations can be significantly limited if they lose access to key habitat areas. Potential effects from the loss of fish passage include loss of genetic diversity by isolation of reaches, loss of range forjuvenile anadromous and resident fish and loss of resident fish from extreme flood or drought events.

There are 638 stream/road crossings in the YoungsBay watershed (Table 5). ODFW conducted a survey of culverts for state and county roads. Of the 36 culverts surveyed by ODFW, 29 did not meet standards, suggesting that they block access to critical habitat areas. Many of these impassable culverts occurred in the lower portions of the watershed blocking access to rather large areas of the watershed. The data did not identify whether the culverts were impassable under all environmental conditions (i.e. low flow, high flow). Current data suggest that impassable culverts are a widespread problem in the YoungsBay watershed. Culverts blocking access to critical fish habitat areas need to be upgraded to improve fish passage.

Table 5.Fish Passage Barriers in YoungsBay Watershed (Bischoff, et al.

2000).

Most of the natural fish passage barriers that occur in the YoungsBay watershed are water falls. Many of the tributaries to the Lewis & ClarkRiver have falls including Stavebolt Creek, Hartill Creek, and Klickitat Creek. There is a possible fish passage barrier at low flows on the mainstem Lewis & ClarkRiver just above the confluence with the Little South Fork and the SouthForkLewis & ClarkRivers. There is also a large falls on the mainstem Lewis & ClarkRivernear the headwaters. There is a falls on the YoungsRiver a little over a mile upstream from where the river flows into the bay. There is also a 25 ft falls on the SouthForkKlaskanineRiver.

A reservoir with an adequatefish ladder is located a few miles upstream from the South Fork confluence on the Lewis andClarkRiver. The Klaskanine fish hatchery blocks the North Fork of the North Fork Klaskanine. Although the hatchery dam is a barrier, there is a fish trap at the North Fork Klaskanine Hatchery; unmarked coho should be passed upstream of the dam.

Table 6.Summary of Life Stages and VSP Parameters Affected.

Life
Stages
Affected / Egg to Parr / Parr to Smolt / Smolt to Adult
Incubation / Early Rearing / Summer Rearing / Winter Rearing / Downstream Migration / Estuary Rearing / Ocean Residence / Upstream Migration / Spawning
X / X / X / X
VSP Parameters Affected / Abundance / Productivity / Diversity / Spatial Structure
X / X / X

Riparian Condition

Riparian vegetation was categorized as having a high, moderate, and low potential for large woody debris recruitment. Vegetation classes defined as coniferous or mixed in the large class (>24 inch dbh) had a high potential for LWD recruitment. Coniferous or mixed vegetation in the medium size class (12-24 inch dbh), and hardwoods in the medium to large class, had moderate potential for LWD recruitment. Almost half of all the subwatersheds in the YoungsBay watershed were considered inadequate for LWD recruitment, with the remaining half typically in the moderate category (Table 7). None of the riparian areas in the YoungsBay watershed demonstrated an adequate potential to contribute LWD to the stream channel. These conditions are likely the result of heavy historical clearcutting for timber in the watersheds, generally leaving the forests in a regenerative state (small to medium conifers). Several of the lower elevation

subwatersheds (Lower Lewis & Clark, Youngs Bay Mouth, Youngs Bay East) had riparian wetlands accounting for 16 to 46 percent of the riparian areas. Although wetlands may or may not contribute LWD to the stream channel depending on the wetland type, they do provide several important habitat features such as back channels and cover. Many of these wetlands are diked and disconnected from the stream limiting access to this habitat.

Table 7. Potential Large Woody Debris Recruitment in the YoungsBay Watershed (Bischoff, et al. 2000).

Table 8.Summary of Life Stages and VSP Parameters Affected.

Life
Stages
Affected / Egg to Parr / Parr to Smolt / Smolt to Adult
Incubation / Early Rearing / Summer Rearing / Winter Rearing / Downstream Migration / Estuary Rearing / Ocean Residence / Upstream Migration / Spawning
X / X / X / X / X / X
VSP Parameters Affected / Abundance / Productivity / Diversity / Spatial Structure
X / X / X / X

Water Quality

Table 9 is a summary of water quality conditions in the YoungsBay watershed.

Table 9.Water Quality Impairment Summary for YoungsBay Watershed

(Bischoff, et al. 2000).

Oregon’s 2002 303(d) list of water quality limited streams included the following water bodies: Klaskanine River (river miles 0-2.7, dissolved oxygen), Lewis and Clark River (river miles 0-10.8, dissolved oxygen and river miles 8.6-10.8, temperature), Skipanon River (river miles 0-2, dissolved oxygen), andYoungs River (river miles 9-23.2, temperature) (ODEQ 2005).

The percent of the land area of the YoungsBay watershed affected by logging, agriculture, and urban development land use is shown in Table 10.

Table 10.Percent Area of the YoungsBay Watershed by Selected Land Uses (Bischoff, et al. 2000).

Temperature

Relatively few (5.4 percent) of the data points at the DEQ ambient monitoring sites exceed 18° C, but many more (31.6 percent) exceed the criterion at the site near Fort Clatsop. The data suggest that the rivers in the Youngs Bay watershed are not impaired in their upper reaches, but show moderate impairment in the lower reaches(Tables 11, 12, and 13) (Bischoff, et al. 2000).

Table 11.Temperature data collected in the Youngs Bay Watershed. Horizontal lines mark evaluation criteria of 13°C (spawning) and 18°C (rearing and migration). Not shown is the criterion of 16°C for core cold water habitat.

Table 12.Temperature data collected in the Youngs Bay Watershed. Horizontal lines mark evaluation criteria of 13°C (spawning) and 18°C (rearing and migration). Not shown is the criterion of 16°C for core cold water habitat.

Table 13.Temperature data collected in the Youngs Bay Watershed. Horizontal line marks evaluation criteria of 13°C (spawning). Not shown is the criterion of 16°C for core cold water habitat.

Nutrients

Phosphorus

Twenty-eight percent of the samples exceeded the evaluation criterion of 0.05 mg/L total P as shown in Table 14. Horizontal line marks evaluation criteria of 0.05 mg/L.

Table 14.Total Phosphorus Data Collected for the YoungsBay Watershed

(Bischoff, et al. 2000).

Nitrate-Nitrogen (NO3-B)

Forty-seven percent of the samples exceeded the evaluation criterion of 0.30 mg/L as shown in Table 15. Horizontal line marks evaluation criteria of 0.30 mg/L.

Table 15.Total Nitrate Data Collected in the YoungsBay Watershed.

Toxics

There are no data available to assess the water quality condition with regard to toxics.

Table 16.Summary of Life Stages and VSP Parameters Affected.

Life
Stages
Affected / Egg to Parr / Parr to Smolt / Smolt to Adult
Incubation / Early Rearing / Summer Rearing / Winter Rearing / Downstream Migration / Estuary Rearing / Ocean Residence / Upstream Migration / Spawning
X / X / X / X / X / X
VSP Parameters Affected / Abundance / Productivity / Diversity / Spatial Structure
X / X / X / X

Water Quantity

Typically, water is diverted from the mainstem Lewis andClarkRiver (25 cfs appropriated) in the months of June through September, and all fourstreams are used in the winter, depending on water quantity and quality. Big and Little SouthForks have 5 cfs of water appropriated for municipal water supply, while only 2 cfs areappropriated for Camp C Creek. The largest withdrawals on the Lewis andClarkRiver are formunicipal and domestic uses, representing 97 percent of the total withdrawals (Table 17).

Table 17. Dewatering Potential in the YoungsBay Watershed based on 50 percent exceedence*.

Table 18.Summary of Life Stages and VSP Parameters Affected.

Substrate

Although sediment sources are highly variable across the YoungsBay landscape, it is likely that land use practices are increasing sediment loading into surface waters (WPN 1999, cited in Bischoff et al. 2000). Many road culverts have been identified to be at risk of causing damage to the stream network. Additionally, road densities are high within 200 ft of the stream, although very few of these are on slopes greater than 50%.

Bischoff et al. (2000) determined that slope instability, road instability, and rural road runoff were the most significant sediment sources based on the location of the watershed (OregonCoastRange, where shallow landslides and deep-seated slumps are common) and local land uses.

The Lewis and ClarkRiver originates in the SaddleMountain area and flows in a northerly direction, finally emptying into YoungsBay. The river is about 25 miles long, of which the lower six miles is a tidal slough. The 7.5 miles of the river from tidewater to a deep canyon section has low banks that are usually flooded each spring. This part of the river is bordered by pastureland and brushy slopes. The canyon is approximately one mile long and very steep. The remainder of the upriver section is covered by second growth and partially logged off land in the hills. The riparian area is generally bordered by alders

The gradient is moderate in the lower section, increasing to fairly steep upstream. The area within the box canyon and up to the Crown Zellerbach bridge (~ 3 miles) is about 40 percent bedrock and 60 percent large boulders, affording no spawning area. The remaining length ofstream averages 5-10 percent gravel.

Table 19.Summary of Life Stages and VSP Parameters Affected.

Life
Stages
Affected / Egg to Parr / Parr to Smolt / Smolt to Adult
Incubation / Early Rearing / Summer Rearing / Winter Rearing / Downstream Migration / Estuary Rearing / Ocean Residence / Upstream Migration / Spawning
X / X / X / X / X
VSP Parameters Affected / Abundance / Productivity / Diversity / Spatial Structure
X / X / X / X

Hatchery

CEDC (Clatsop Economic Development Commission) Net Pen Coho Program

Coho production for this program was from the Eagle Creek NFH coho program until 2004. Currently production is from the Bonneville Hatchery (TannerCreek stock) coho program. Broodstock is collected and reared at this facility. The coho program is designed to be isolated from the reference population. This program supports a terminal fishery targeting returning coho salmon. The net effect of this program on the reference population is uncertain. Most of the naturally spawning coho salmon are marked hatchery fish, and the small proportion of the naturally spawning population that are unmarked are progeny of hatchery coho. Peak spawning counts for coho were near zero for most of the 1980s and 1990s (NMFS 2004).

AstoriaHigh School (STEP) Coho Fry Program. (Big Creek Hatchery Coho) and WarrentonHigh School (STEP) Coho Fry Program. (Big Creek Hatchery Coho)

The eggs for these programs are from the Big Creek Hatchery coho program and are not part of the YoungsBay population. The eggs are derived from coho returning to Big Creek Hatchery and are not integrated with the reference population. These programs are primarily for educational purposes and are not expected to increase abundances. There is the potential for loss of diversity if these program fish from the Big Creek population survive to contribute to the naturally reproducing coho salmon in YoungsBay (NMFS 2004).

Table 20.Summary of Life Stages and VSP Parameters Affected.

Life
Stages
Affected / Egg to Parr / Parr to Smolt / Smolt to Adult
Incubation / Early Rearing / Summer Rearing / Winter Rearing / Downstream Migration / Estuary Rearing / Ocean Residence / Upstream Migration / Spawning
X / X / X
VSP Parameters Affected / Abundance / Productivity / Diversity / Spatial Structure
X / X / X / X

Works Cited

Bischoff, J. M, R. B. Raymond, K. U. Snyder, L. Heigh, and S. K. Binder. 2000a. YoungsBay Watershed Assessment. E&S Chemistry, Inc. and YoungsBay Watershed Council, Corvallis, OR. August.

LCEP and LCFRB (Lower Columbia Estuary Partnerships and Lower Columbia Fish Recovery Board). 2004. Mainstem lower Columbia River and Columbia River estuary subbasin plan. Prepared for the Northwest Power and Conservation Council. May.

McElhany, P., T. Backman, C. Busack, S. Kolmes, J. Myers, D. Rawding, A. Steel, C. Steward, T. Whitesel, and C. Willis. 2004. Status evaluation of salmon and steelhead populations in the Willamette and lower Columbia basins. Willamette/Lower Columbia Technical Recovery Team. National Marine Fisheries Service, NorthwestFisheriesScienceCenter.

National Marine Fisheries Service (NMFS) 2004. Salmonid Hatchery Inventory and Effects Evaluation Report.

Oregon Department of Environmental Quality (ODEQ).

Accessed November, 2005.

[1] “Channel stability measures the channel’s ability to move laterally and vertically and to form a ‘normal’ sequence of stream unit types” (LCEP and LCFRB 2004).