Operational Plan

JUVENILE SALMON REARING AND MIGRATORY HABITATS OF THE FOXRIVER FLATS ESTUARY

Period Covered: April 15, 2009 to July15, 2009

Principle Investigator: / Coowe Walker, Habitat Biologist II
Assisting Personnel:
KBRR: / Angela Doroff, Fisheries Biologist III
Steve Baird, Research Analyst II
Univ. of Washington / Professor Charles Simenstad, consulting
Biometrics : / Adam Craig
Titles / Approval Signatures / Date
Project Biologist:
Consulting Biometrician:
Regional Research Supervisor
Regional Supervisor:
Final Biometric Review:

TABLE OF CONTENTS

LIST OF FIGURES

LIST OF TABLES

LIST OF APPENDICES

INTRODUCTION

Description of Project Area

GOALS AND OBJECTIVES

STUDY DESIGN

Salinity intrusion. (Objective 1)………………………………………………………………......

Study Sites (Objective 2)

Site Selection

Sample Size

DATA COLLECTION

Salinity Gradient (Objective 1)

Study Site Identification (Objective 2)

DATA PROCESSING

Salinity Gradient (Objective 1)

Study Site Identification (Objective 2)

DATA ANALYSIS

Salinity Gradient (Objective 1)

Study Site Identification (Objective 2)

SCHEDULES

REPORTS AND PRODUCTS

RESPONSIBILITIES

LITERATURE CITED

LIST OF FIGURES

Figure 1. Overview of the Fox River Flats Critical Habitat Area.

Figure 2. Image identifying study site andl habitat types

LIST OF TABLES

Table 1. Data collection dates for the 2009 field season.

LIST OF APPENDICES

Appendix A 1. ADF&G Fish Sampling Data Form...... 16

AppendixA 2. ADF&G Water Quality Data Form...... 17

1

INTRODUCTION

Estuarine habitats are important in the life cycle of anadromous salmon, providing vital habitat during periods of physiological transition as adults return to spawn and as juveniles outmigrate to the ocean (Simenstad et al. 1982; Healey 1982; Levings et al. 1986; Quinn 2005). The diverse habitats of estuaries include river channels, salt marshes, non-vegetated mudflats and dendritic tidal channels, which provide wide ranging physical and chemical conditions including variable turbidity, depth, salinity, temperature and velocities. In the Pacific Northwest, dramatic losses of estuary habitats have been linked to declines in Pacific salmon populations, leading to costly, and questionably effective, estuary restoration efforts (Simenstad 1997; Simenstad and Cordell 2000).Subsequently a lot of attention has focused on how juvenile salmon use estuaries in the Pacific Northwest. Alaska remains a stronghold of healthy salmon populations at present. However, these fish are susceptible to the same threats that have led to their collapse elsewhere. Studying salmon in Alaskan estuaries will provide science to support conservation and ensure the sustainability of salmon into the future.

Depending on species and size, juvenile salmon will spend as little as a few hours to more than 12 weeks in estuaries(Healey 1982; Simenstad et al. 1982; Levy and Northcott 1982). McMahon and Holtby (1992) found that distribution of juvenile salmon within estuaries was related to salinity gradients,theavailability of cover and production of prey organisms. McMahon and Holtby (1992)hypothesized that estuaries which providehabitat with ample cover, food, and gradual salinity gradients that allow for optimal osmoregulatory adaptation may improve ocean survival of juvenile fish. Research also suggests that tidal inundation levels are an important driver of estuarine habitat conditions, with higher tide levels generating greater tidal channel density, and more diverse vegetation communities, benthic invertebrates and insects (Simenstad and Cordell 2000).

Here we put forward a feasibility plan for identifying and accessing habitats in a southcentral Alaska estuary, the Fox River estuary at the head of KachemakBay. This plan will be the first step towards building a research program aimed at developing an understanding of the importance of estuarine habitats to outmigrating juvenile salmon in this estuary. Our project is necessarily exploratory because so little is currently known about the area. Because the extreme tidal range of Kachemak Bay (28+ feet), creates considerable challenges for access and sampling techniques, this operation plan will focus on identifying habitats within the Fox River Flats that can be reliably sampled over time. To date, there has very little research in this area, and the only research examining salmon use was completed in 1985-86, and limited to upstream migration of adult salmon (Faurot and Palmer 1992).

Funding for this research is provided through a State Wildlife Grant to the Kachemak Bay Research Reserve to investigate juvenile salmon use of the Fox River estuary. This research will expand our understanding of the importance of estuaries to juvenile salmon life histories to include a high latitude estuary with extreme tidal ranges and freezing temperatures, and will yield the first baseline information on juvenile salmon use of the Fox River estuary.

Description of Project Area

In 1972, the Alaska State Legislature designateda portion of the Fox Riverestuary as a Critical Habitat Area (CHA) for the protection of fish and wildlife habitat, with the official name of the Fox River Flats CHA (Figure 1). The Fox River and Sheep River (the other major river that empties into the head of Kachemak Bay in the Critical Habitat Area), are by far the largest river systems draining into Kachemak Bay (KBRRand NOAA 2001), and are therefore likely to provide a significant amount of salmon spawning and rearing habitat for fish that return to Kachemak Bay. The Fox River is a major river originating in the KenaiMountains discharging at the base of Chernoff Glacier, and takes in several tributaries before emptying into KachemakBay. The Fox River Flats CHA is within the boundary of the Kachemak Bay Research Reserve (KBRR), established in 1999 as part of the National Estuarine Research Reserve System (NERRS). Like other NERRs, KBRR conducts long-term ecological research and education, especially emphasizing research that will benefit long-term stewardship of the Bay’s ecosystems.

The actual delta for the Fox River is an expansive complex of intertidal mud flats and low-lying marshlands, encompassing approximately 7.7 square kilometers and 6.6 river miles, and extending beyond the legislatively designated of the Fox River Flats CHA (Figure 2). Anadromous runs of coho (Onchorynchus kistuch), chum (O. keta), pink (O. gorbuscha) and sockeye (O. nerka) salmon, as well as Dolly Varden (Salvelinus malma) are supported in the Fox River. At the top of the delta, the river flows in one main channel. As the gradient levels into the intertidal area, the river forms a braid, consisting of one main channel and two side channels with multiple lateral tributary channels associated with the main and side channels. There are also several tidal channels near, but not connected to the Fox River that may provide juvenile fish habitat.

Figure 1. The Fox River Flats Critical Habitat Area located at the head of KachemakBay in south central Alaska

Human Use Patterns

The Fox River Flats CHA has historically been used by ranchers, hunters, and all terrain vehicle (ATV) enthusiasts. Access can be found at Swift Creek Switchback Trail at the end of East Road where a switchback trail, authorized by the State for pedestrian, horse, and ATV access only, leads down to the beach. There are numerous private properties surrounding the CHA, including the Russian Old Believer villages of Kachemak Selo, Razdolna and Vosnesenka. There are also several private parcels that are being developed as seasonal residencesin the Fox River valley, which require access through the Fox River estuary Cattle have been grazed on the estuary marshlands since 1961 through a lease agreement between the cattlemen and the State (Sonnen 2004). The current 25-year lease ends in 2020. Several studies were conducted prior to the most recent grazing lease renewal to investigate the effects of grazing on plant communities. The studies included exclusion experiments, assessment of cattle utilization, evaluation of plant annual production, ecological site mapping (basic plant communities and soils), and visual reconnaissance assessments by several biologists. The results of these studies indicate that cattle prefer to graze the intertidal sedge communities and to use upland areas for loafing. While past studies through the Natural Resources Conservation Service have shown the Fox River Flats CHA to have a carrying capacity of 800 head of cattle, only 300 range the area at this time. ATV use in the CHAhas become more prevalent over the past several years. Hunters access the area generally in the fall, by ATV, boat and airplane; residents of the local villages and adjacent landowners access the CHA year round.

GOALS AND OBJECTIVES

The overall goal for this first year of the project is to identify study sites that can be repeatedly sampled for juvenile salmon over time in the Fox River Flats. This is year one of an ongoing project that will extend over at least two years.

Specific objectivesfor this year are:

  1. Establish salinity gradient zones in the Fox River Flats such that areas of low, medium and high salinity can be delineated.
  2. Identify study sites representing five habitat types within salinity zones that can be accessedand sampled for juvenile fish throughout time.

Task: Collect five individuals of each species from each habitat type and each sampling event for stomach content analysis to be led by the University of Washington.

STUDY DESIGN

We will target five habitat types and four salinity zones that juvenile fish are thought to respond to, and utilize juvenile salmon sampling techniques (beach seines and modified fyke nets) that have been successful in the Pacific Northwest to determine if they are effective here (Dr.Charles Simenstad personal communication). Establishing which habitats can be sampled at different tides will provide the baseline for long term research in the Fox River Flats CHA.Data collection for this project will take place between May and mid July, 2009. This time period broadly brackets the timing of juvenile coho salmon outmigration and estuarine residence in south-central Alaska (Faurot and Palmer 1992; Eskelin 2004; Moulton 1997). There will be a total of sixsampling events, two per month, beginning in May.

Figure 2. 2005 aerial image of the study area within the lower Fox River (a subset of the Fox River Flats CHA) taken at low tide indicating the five main habitat types we are interested in sampling. Red lines show the Critical Habitat Area boundary.

Site Selection

We will assess the feasibility of sampling five different habitat types in our study area (Fig 2)

  1. Fox River Main Channel (MC),
  2. Fox River Side Channel (SC). The Fox River splits off into two side channels adjacent to the main channel shortly after flowing onto the Flats. We will use the westernmost side channel as our side channel sampling habitat because access is likely easier.
  3. Tributaries associated with the main channel (TMC). Two tributary habitats off the MC will be sampled.
  4. Tributaries associated with the side channel (TSC). Two tributary habitats off the MC will be sampled.
  5. Tidal channels unassociated with the river (TC). Two tidal channels not associated with the river will be sampled.

salinity gradient (Objective 1)

Salinity gradients will be sampled in all five habitat types.

At the beginning of the study season, rapid salinity assessments will be made longitudinally, using a YSI data sonde, in the MC and SC at ten evenly spaced locations to establish salinity ‘zones’ based on practical salinity units (psu);

  • tidal freshwater: water level variation with tide, but no salinity;
  • oligohaline (low): 0.5-3 psu;
  • mid-salinity ranges: 3-18 psu; and
  • euhaline and mid-upper salinities: 18-30 psu.

In the MC, longitudinal measurements will be made from the mouth of the river, where it enters KachemakBay to the landward extent of tidal influence (made by visual observation). In theSC, longitudinal measurements will be made from the mouth of the channel, where it flows into KachemakBay upstream to the confluence of the side channel and the main channel. In the tributary habitats (TMC and TSC), and the tidal channels not associated with the river (TC), salinities will be measured at the confluence and at the head of the channels. If there is a difference in salinities between these two points, then a more detailed gradient will be sampled in between these two points. Once the four zones are established, detailed salinity/temperature profiles will be taken within each zone.

Rapid assessment will involve one reading near the surface and one near the bottom of the channel. Detailed profiles will be obtained at three points within each salinity zone using a SeaBird Electronics SBE-19plus Seacat CTD (conductivity, temperature, depth) sensor and will be recorded on the “ADF&G Water Quality” data form (Appendix A1).

identify styudy sites(Objective 2)

Once salinity zones have been established, we will determine which habitat types are present in each zone, how to access the different habitat types, when the habitat types are available and what methods and gear are best used to capture fish in each habitat.

Beach seines will be used in river channel habitats and modified fyke nets will be used to sample fish in tidal channels and marshes. The fyke nets are placed near the mouth of small tidal channel at high tide. Fish move out of the channels as the tide recedes and are caught in the cod end of the fyke net. This technique makes it possible to sample fish use of marsh surfaces adjacent to tidal channels when tides are high enough to permit fish access from the channel to the marsh surface (Simenstad et al. 1982), however we do not know whether these techniques will work with the large volumes of water that are associated with the substantial tidal range of Kachemak Bay.

Fish will be sampled in the MC and SC salinity zones using seine nets deployed from a river boat. The TSC, TMS and TC habitats will be sampled for fish using modified fyke nets. Salinities will be measured in each established zone prior to fish sampling.

Each sampling event will take five days, using the following schedule:

Day 1: main river channel habitats (all salinity zones)

Day 2: side river channel habitat (all salinity zones)

Day 3: tidal channel habitats (n=2)

Day 4: high salinity off-channel tributary habitats

Day 5: low salinity off-channel tributary habitats

Fish sampling will take place bi-monthly at a range of high tide levels in order to determine when habitats are accessible (Table 1). Fish sampling will take place during high slack tides, (2 hours from high tide). The tidal stage will be recorded at each sampling location at the time of sampling.The tide elevation will be obtained by utilizing the tide page on the GPS unit and by ensuring that the “nearest tide station” has been selected. Notes on access and gear deployment will be included on the data forms. These samples will provide estimates of the timingand relative density of juvenile salmon using the different habitat types, and will make clear when habitats are clearly accessible for successful sampling.

Main and Side Channel Habitats

We will use a beach seine to conduct comparative instantaneous (“grab”) samples of fishes in the channel habitats. To deploy the seine, two people will be on land to hold one end of the seine while two people will remain in the boat to set the seine. The seine will be deployed parallel to shore and once the net is set, it will be hauled to the beach by lines attached to each end of the seine.

Tributary Habitats

A modified nylon mesh (0.6 cm) fyke net will be deployed across each discrete tide channel at high, slack tide (Gray et al 2002). As the tide recedes, the fish will be collected from the cod end of the net, identified, and counted. Pole seining will be used to“herd” residual fish into the trap where marsh channels fail to dewater completely at low tide. This trapping technique has been used successfully by Levy and Northcote (1982) in the FraserRiver estuary and by Simenstad et al. (1997), Miller and Simenstad (1997) in the ChehalisRiver estuary, and Bottom et al. 2005a in the Salmon River estuary.

Upon recovery of the nets all fish will be identified, counted, and measured for fork length (to the nearest 1.0 mm) and weighed. Comments will be recorded describing physical characteristics of the fish, and photos will be taken.

All data associated with fish sampling will be recorded on the “ADF&G Fish Sampling” data form (Appendix B1).

Sample Size

Sites will be considered feasible for future research efforts if they can be reliably sampled at all seven sample periods.

DATA COLLECTION

Data Management

Prior to field activities, hardcopy color maps will be printed out for field use. Maps will identify channel and off-channel tributary habitat sampling locations throughout the study area. Once the salinity zones have been established, waypoints identifying sampling locations will be uploaded to a Garmin GPS 76. The Garmin GPS 76 is WAAS-enabled for accuracy to within 3 meters, 95 percent of the time (Garmin Ltd., 2007). Observers will navigate to sampling locations using the “GOTO” function on the GPS.