The Cowichan

The Cowichan Watershed drains an area of approximately 939 km² and flows 47km from its headwaters at Cowichan Lake, among the peaks of the Vancouver Island Ranges, through forests and fields to the estuary at Cowichan Bay^[1]. Abounding with diversity and biological value, the Cowichan River was designated a BC Heritage River in 1996 and a Canadian Heritage River in 2003^[2].

The Cowichan River supports a rich variety of biological values that are characteristic of southeastern Vancouver Island. It is considered one of the most valuable and productive salmon and trout streams on Vancouver Island, supporting a host of native fish species including chinook, which are the special focus for this report.

The Cowichan River watershed also provides habitat for an array of wildlife species native to Vancouver Island. Black-tailed deer, black bear and cougar are relatively common, while Roosevelt elk and wolf are more rarely seen. Many small mammals ranging from otter to shrews, beaver, marten, mink, weasel, raccoon, red squirrel, bats, shrews and voles. The valley over 200 species of birds, including osprey, bald eagles, ravens, hawks, owls and ducks. The Cowichan Estuary provides important winter habitat for thousands of waterfowl, is crucial habitat for juvenile salmonids and many other marine fish and invertebrates.

Vision of the Cowichan Watershed

Water is integral in every component of our lives and is central to our societal, cultural and spiritual needs. Healthy watersheds have become a focus of many communities as they embrace policies and plans that reflect a new relationship to water that ensures ecosystem health and a reliable and safe water supply for human use including a thriving economy. Watersheds also span the human construct of boundaries that are established by local governments and cities. Working together to ensure healthy watersheds has become the focus of government agencies and citizens alike. The Cowichan has many of the key Conditions for Success.

In the Cowichan Valley, First Nations, federal, provincial and local governments, local interest groups, and residents, in collaboration, have together agreed to a common vision and have committed to restore the Cowichan River watershed and facilitate the recovery of its fisheries(see visioning document for a list of vision statements). Cowichan Tribes and Fisheries and Oceans Canada have partnered in the development of this initiative aimed at watershed health and Chinook in the Cowichan, with the opportunity to implement the Federal Wild Salmon Policy framework and goals and Cowichan Tribes Indigenous governance at a local level. The objective is to foster a “made in Cowichan” solution. Other partners, such as the Cowichan Valley Regional District (CVRD), the Cowichan Watershed Board (CWB) and the Cowichan Stewardship Roundtable have been key players in the inception of this Initiative and will be critical to its on-going implementation and success.

We see this initiative providing opportunity to collectively help manage local water resources affecting biological communities and empower the citizens of Quw’utsun’ - the Cowichan Valley - to work together in the restoration of the river, the chinook, and achieving their shared vision for watershed health.

Vision of a Healthy Watershed

A healthy and biologically rich Cowichan Watershed reflecting the wisdom, stewardship and vision of its informed citizens, organizations and community institutions working closely together (CSRT, ToR 2014)

For a forward looking view of the watershed see the Watershed Vision from the Eye of an Eagle

Watershed Health Goals

Healthy watershed ecosystems contribute directly and indirectly to our human well-being, our survival, and our quality of life. They also contribute socio-cultural, societal and environmental benefits. Both natural landscape and human activities create pressures affecting watershed health.

The people of the Cowichan Valley see, use and experience the Cowichan River in many ways. The watershed and the water in it is one of our most valuable assets. It’s intrinsic value cannot be quantified, however, providing estimates of the annual contribution of ecosystem services supporting the quality of life in the Cowichan provides reasons for decision-makers to protect and conserve those values. Defining ecosystem services and choosing indicators is still under development.

Values	Indicators
How do you value Ecosystem Services?
Supporting	Supply
Provisioning	Delivery
Regulating	Contribution to well-being
Cultural	Economic Value

We provide 4 watershed goals, reflecting the 4 attributes of watershed health: hydrology, physical habitat, biological communities, and water quality. The following goals will shape how we describe, plan, manage and monitor our efforts toward achieving the vision of watershed health.

Figure 1: Watershed Health Attribute Goals

Every year the Quw’utsun’ people were assured great riches as the spawning salmon returned to the Cowichan, Koksilah, and other rivers and streams. Our Elders carefully managed the harvest and sharing of fish through the use of fish weirs, a gift from the First Ancestor Syalutsa. The weirs ensured abundant food for our people to eat, while allowing enough fish to reach the spawning beds to ensure future returns. Other resources were equally managed with an eye to future abundance. The watershed was healthy and sustained us.”

Chief William Seymour

Fish Weir. Courtesy of Royal BC Museum Archives

“Conservation is not a trade-off between the economy and the environment. It is a trade-off between short and long term.”

Dr. Carl Safina

Framework for Assessing Watershed Health

Healthy watersheds and the factors affecting their health have been described in many watershed-planning processes (Portland, 2005; NOAA, 2009; Conservation Ontario, 2003). Many of these processes use general state indicators, such as forest cover, surface water and ground water to describe watershed health. In this report we use a more local-scale model, borrowing heavily from the Portland Watershed Management Plan (2005) to provide a framework and scientific foundation. Four general areas of interest (hydrology, physical habitat, water quality and biological communities) are proposed as focal attributes to manage for in the Cowichan Watershed. For each attribute a series of state indicators are proposed (Figure 1).

The pressures and state indicators are reviewed in terms of their impact on salmon productivity in the Cowichan. This was done by understanding the how watershed pressures (or threats) affect watershed health and salmon production, quantifying the current status of chinook stocks using an expanded version of the Wild Salmon Policy Conservation Unit (CU) stock status methodology, identifying the critical habitat and critical limiting factors to production using quantitative field data (if available) and an iterative qualitative expert process called a Risk Assessment Procedure (Pearsall et al, in progress). Action plans were then developed to address critical limiting factors to production of chinook. Governments and stakeholders are working to develop integrated strategic plans and explore governance models for watershed management.

State of the Environment Report (CVRD, 2010)

The State of the Environment Report (SOE) reviewed the status of a variety of environmental indicators and issues that track the health of the environment within the Regional District, with Salmon being one of the key indicators. The Report indicates that the natural landscape has been dramatically altered, with over 75% of the land-base having some human alteration. As a result many native species and ecosystems are at-risk as regional climate shifts and other species are introduced. Water quality and quantity remain a concern, while the region’s air quality is often suspected of inducing high hospital admission rates. These shifts in climatic factors are thought to be causing increased frequency of drought and flood events on Southern Vancouver Island.

The Watershed Health and Chinook Initiative builds on the SOE, focusing in on Chinook salmon as a key indicator of watershed health.

Figure 2: Framework for Watershed Health (adapted from Portland, 2005)

Watershed Pressures

Often referred to as threats, describe the natural processes and human activities that impact, stress or pose a threat to environmental quality and watershed health.

Watershed Attributes

Are broad overall categories that can be used to describe the state of the environment, the quality and quantity of natural resources, and the state of human and ecological health.

Watershed State Indicators

Are the detailed indices that can be used to quantify watershed health, chosen by considering biological, chemical and physical variables and ecological function.

Chinook As A Key Indicator

Chinook smolts being released into the river

Salmon are highly sensitive to all components of watershed health (hydrology, habitat, water quality and biological communities). They are considered a key indicator species, meaning that their presence or absence is central to many other physical, chemical and biological processes in an ecosystem (Portland 2005,LGL, 2005; CVRD, 2010).

Chinook are present in the Cowichan River almost the whole year as either spring or fall returning adults, eggs in the gravel, fry or smolts. They are distributed throughout the entire river, and are in Cowichan Lake and the upper tributaries. Chinook are sensitive to changes in their critical habitat (i.e. water quality and quantity, gravel substrate mobility and accumulations, cover to limit predation, and food). Each of the watershed health attributes (hydrology, physical habitat, water quality and biological communities) affect one or more of the life stages of Chinook in fresh water. For this report Chinook salmon productivity (adult recruits produced by each spawner) and abundance are used as key indicators. For the period of 1995-2006 Cowichan Chinook were in a serious decline. Natural mortality during the fresh-water and early marine stages were 90 and 99% respectively. Fishing mortality was also at 70% (Figure 3).

Ecosystem Unit	Life Stage	Chinook	Mortality	Chinook	Mortality
		Declining 1995-2006		Rebuilding 2009-Present
Estuary to upper river	Migrating adults	3,000	20%	3,000	20%
upper river - uplands	Spawners	2,400	20%	2,400	20%
upper river - uplands	Eggs laid	4,440,000	90.0%	4,440,000	85.0%
lower river to estuary	Smolts out	444,000	90.0%	666,000	85.0%
Estuary to Ocean	Adults produced	4,440	99.0%	13,320	98.0%
Ocean	Caught in ocean	3,108	70%	7,992	60%
Estuary to upper river	Terminal return	1,332	-	5,328	-
	Rate of change	-56%		78%
	Recruits/spawner	0.56		2.22

Figure 3: Typical mortality during each life-history stage for Cowichan chinook in a declining phase from 1995-2006 and in a rebuilding phase from 2009 onwards.

Since 2009 (adult return year) Cowichan chinook have begun to re-build. This is likely due to reduced freshwater mortality producing more smolts and improved growth, through work such as Stoltz Bluff remediation and improved access to off-channel habitat in the lower river for rearing. The result was healthier and more robust smolts were leaving the river. This contributed, along with improved marine conditions, to slightly reduced marine mortality. Reductions in marine harvest from 70% to 60% also helped in rebuilding. Abundance of Cowichan chinook reached the DFO target of 6,500 spawners in 2016 for the first time in many years.

Status Of Watershed Attributes and State Indicators

In 2013, the DFO habitat report card for East Vancouver Island: Cowichan/Koksilah Conservation Unit assigned the cumulative watershed risk score as High Risk (or RED)^[6]. In this initiative we try and deepen our understanding of the pressures (or threats and risks) that affect watershed health by measuring indicators of the four attributes of watershed health. This will help us achieve our collective vision of a healthy and biologically rich Cowichan Watershed. The full status of the Cowichan watershed has not been assigned and further work is needed. However, we are starting the process by looking at the status of the watershed through the lens of chinook. State indicators and their effect on Cowichan chinook productivity are summarized for each of the watershed health attributes and goals. An interim status is assigned.

Hydrology Goal - Move toward normative* flow conditions to protect and improve watershed and stream health, channel functions, and public health and safety.

Low flows in the early summer through fall limit Chinook access and increase predation impacts

Issue - Water management is steadily becoming an issue of increasing importance due to the anticipated effects of drier summers as a result of climate change, coupled the the increasing demand for water to satisfy forecasted population growth. In the Cowichan Valley, given current trends, the population is predicted to increase by 27% over the next 25 years(Westland 2005). Currently, human water withdrawals greatly exceed inflows from precipitation or snow-melt during the period of summer low flow. This increases the risk that there is insufficient water storage to sustain fisheries values, ecological values, recreational opportunities and flows required for dilution of effluents in the lower river (Nelitz 2007). Projected water demands for the fall of 2031, (assuming low precipitation flow scenario) will be 4 times greater than the amount of water currently flowing into the system (Westland 2007).

Figure 4: Historical low flows at WSC station 08HA002 below Cowichan Lake (Chapman 2010).

Hydrograph Alterations and Flow Management - an ad hoc multi-interest committee known as the Cowichan River Committee cooperatively engaging on managing water flows in the river. The group includes of the Cowichan Tribes, Catalyst Paper, Fisheries and Oceans Canada (DFO) and Forest, Lands and Natural Resource Operations (FLNRO). The group collectively makes in-season flow management decisions during times of annual drought. The ability to sustain adequate maintenance flows is dependent on available water storage in Cowichan Lake and precipitation during the regulation period. Recent studies indicate that seasonal inflows appear to be declining over the past several decades. The Cowichan Watershed Board Technical Advisory Committee supports a Flows and Fish Sub-committee that is currently monitoring and examining flows and resulting storage needed to sustain fisheries values in the Cowichan River. Options are being explored to address water management and possibly additional storage needs to counter climate impacts.

Physical Habitat Goal – Protect, enhance and restore aquatic and terrestrial habitat conditions to support key ecological functions and improved productivity, diversity, capacity and distribution of native fish and wildlife populations and biological communities.

Side-channel connectivity, lower river riparian and estuary habitat has been degraded or lost, limiting juvenile rearing areas

Issues -The Cowichan River and Cowichan Lake fish habitats have not been specifically mapped in their entirety. Various studies have been conducted throughout the years with more recent one’s focusing on habitat changes related to flow conditions. Cowichan Tribes has applied for funding from DFO to conduct a critical habitat inventory in 2016-2018. This inventory will define critical habitat and provide an assessment if current habitat is limiting Chinook production.

Floodplain quality and connectivity - The Integrated Flood Management Plan (nhc, 2010) provides an overview of the floodplain quality and connectivity in the lower Cowichan and Koksilah River delta. Significant impacts to the floodplain have occurred with the development of the lower river floodplain for agriculture, commercial and residential areas. Access has been restored to a number of large side channels through a project undertaken by Cowichan Tribes and DFO in the early 2000’s and other partners during dike remediation works in 2012-2016.

Riparian - Riparian areas, especially those wetted during higher flows, are critically important to rearing Chinook fry (BCCF, 2015). The riparian edge habitat along the Cowichan River remains relatively intact for the majority of the upper and mid- river. Recent studies have inventoried areas in the lower river that have been damaged due to increased human development and diking and restoration opportunities have been suggested (Figure 5, LGL, 2005, BCCF, 2016). A full review of riparian critical habitat for Chinook is expected in 2017 through a critical habitat project being undertaken by Cowichan Tribes.

Stream Connectivity - Connectivity issues between the mainstem Cowichan River and its tributaries and side channels occurs as flows are lowered in the late spring (BCCF, 2006). As flows drop side-channels and tributaries start to loose connectivity. Most are completely disconnected at recent flows experienced in May and June of 2016 where flows were 4.5cms in an attempt to conserve water for continual flow through August.

Water Quality Goal - Protect and improve surface water and groundwater quality to protect public health and support native fish and wildlife populations and biological communities.

Extreme summer temperatures in the Cowichan River cause thermal stress for fish and limit Chinook migration

Issue - In the late 1980’s the Ministry of Environment established water quality objectives for the Cowichan and Koksilah Rivers including specific thresholds for various water quality parameters (McKean, 1989). In recent years, water quality objectives have been generally obtained in the Cowichan River (Obee and Epps, 2011 and 2015) however, high summer temperatures coupled with low flows over the past three consecutive summers have been concerns for salmonids and high fecal coliform levels have been recorded in the Koksilah River system.

Temperature and Dissolved Oxygen - The temperature of a stream can affect all life stages of salmonids. High water temperatures can delay upstream migration of adults and cause increased use of thermal refugia. It can also lead to physiological stresses including reduced reproductive success and increased susceptibility to disease, parasites and pollution (Smith, 2015).

Dissolved oxygen (DO) in water is directly related to temperature where DO levels decrease as temperature increases. Migrating fish need at least 80% saturation with temporary levels no lower than 5.0mg/L (Reiser and Bjorn 1979).

Obee (2011) established Ministry of Environment water quality objectives for the Cowichan and Koksilah Rivers setting minimum requirements for eyed or hatched fish at 11.2 mg/L from October to May and for alevins or juvenile fish at 8.0mg/L from June through September. DO levels fell below the MOE recommended guidelines in the Cowichan River on several occasions between 2001 and 2009 although since 2010 levels have exceeded the objectives (Smith, 2015).

Biological Communities Goal - Protect, enhance, manage and restore native aquatic and terrestrial species and biological communities to improve and maintain biodiversity in Cowichan watersheds.

Predation impacts appear to be a very high limiting factor for both adult and juvenile Cowichan Chinook

Issue - The Cowichan basin supports a diverse range of high value ecological features and communities that include rare and sensitive aquatic and terrestrial ecosystems, important fish communities and ecologically significant habitat features. However, species equilibriums have been impacted by development and invasive or introduced species.

Species Interactions - Current research by the UBC Marine Mammal Unit is focused on the role of salmon in pinniped diets. In the Cowichan, pinniped predation on Chinook salmon is hypothesized to be a major contribution to mortality of juveniles entering the estuary as smolts and returning adults holding in the estuary and Cowichan Bay when low flows and/or high river water temperatures prevent migration upstream. Cowichan Tribes is currently undertaking a project to provide relative estimates of predation of Chinook by pinnipeds and it’s significance.

Invasive and Exotic Species - The CVRD’s State of Environment Report uses invasive species as one of the indicators of the health of the environment in the CVRD (CVRD, 2010). This report identified that there are at least 30 invasive plants within the CVRD region.

Other introduced, invasive or exotic species such as pumpkin seed sunfish are found in the Cowichan and Koksilah Rivers. Invasive species can impact habitat for Chinook, compete for resources or are salmonid predators. Bohemian and Japanese Knotweed are of particular interest with respect to changes in riparian habitats caused by this highly invasive plant species. Introduced Brown Trout in the Cowichan River are known to predate on salmonids although impacts of this predation have not been fully quantified. Recent studies suggest a high loss of downstream migrating chinook. Additional work to determine impacts of Brown Trout predation are on-going by Cowichan Tribes and DFO.

Shoreline Ecosystems - Shoreline ecosystems, such as those developed in the Cowichan River estuary and adjacent shoreline, play an important role in the production of Pacific herring, surf smelt and Pacific sand lance. These fish school in large numbers to spawn in intertidal or shallow water habitat in the Cowichan River estuary. These species provide a critical middle link in the salmonid food web, feeding on zooplankton and providing a food source for secondary predators including juvenile and adult salmon, lingcod, rockfish, birds and marine mammals (de Graaf 2010). Sandlance and surf smelt make up 10-50% of the diet of chinook and >50% of the diet of coho (Penttila 2005).

Status of Cowichan River Chinook

Wild Salmon Policy outlines framework for assessing status. Abundance is not the only measure and distribution within the available habitat, genetic diversity, trends, etc. are also metrics used.

Figure 6: Wild Salmon Policy Red, Amber and Green zones used for establishing status

A Red status would indicate a low level of spawner abundance and distribution and therefore the CU would require a high level of management intervention. Similarly a Green status would indicate a high level of spawner abundance and distribution and therefore the CU would require a low level of management intervention. The three status zones are delineated by a Lower and Upper Benchmark. These benchmarks would be defined for each metric used in the status assessment and compared to the CU for status designation (Figure A1).

Estimates are reported for returns of adult spawners to the Cowichan River using a full-span enumeration fence. These estimates and their relationship to abundance targets are a key component of determining the status of Cowichan chinook. We have good knowledge of fall run Cowichan chinook but need more info on early run. A DIDSON counting device was used in the mid-river section of the Cowichan and at the Cowichan Weir at the outlet of Cowichan Lake over the past two spring and early summer periods to estimate abundance of early-run chinook.

For Cowichan River fall run chinook the goal of 6500 adult natural spawners was set by DFO in 2005, based on stock-recruitment analysis, as the spawner level, which on average, should achieve maximum sustained yield (Smsy). This level is used as the higher benchmark separating the amber and green zone (see Figure 5) for management intervention. This is slightly more conservative than the general guidance under the Wild Salmon Policy to use 80% of Smsy. In addition, about 600 chinook are taken each year for hatchery brood stock. Habitat based spawner goals, such as work supported by Cowichan Tribes suggests capacity for at least 8000 adult natural spawners (LGL 2005). The Cowichan Recovery Plan recommended the escapement goal for fall run Cowichan chinook be 12,000 with 8,000 for natural spawners and 4,000 for hatchery brood-stock as a re-building goal in times of low marine survival (LGL, 2005).

The trend in abundance of Cowichan chinook fall adult natural spawners has been increasing since the low in 2009. In 2016 the goal was achieved for the first time since 1997.

Figure 7: Trend in Cowichan River Chinook Spawners from 1988-2016.

Amber/Green Rating for Fall Cowichan Chinook

Based on the abundance metric the current status of Cowichan Fall chinook is amber/green. However, significant critical limiting factors, described below, may continue to limit Cowichan chinook productivity. Actions aimed at resolving these will help in achieving a productive Cowichan chinook population and a healthier watershed.

Critical Limiting Factors

Watershed/Freshwater Factor - In 2013, DFO developed a Risk Assessment Procedure (RAP); a systematic tool to prioritize known habitat and ecosystem based factors limiting chinook production (Pearsall et al 2014, in progress). This methodology was adapted from Hobday (2007) to assess the impacts of stressors or limiting factors (LFs) on the productivity and capacity of a population and its habitat using a life history model. It is used for data-deficient systems and focuses on qualitative information. The RAP helps identify and prioritize limiting factors to salmonid production now and in the future under various climate change scenarios. The primary function of the risk assessment is to describe the relationship between different environmental attributes and measures of biological performance. More details on this methodology can be found in the Cowichan Risk Assessment Backgrounder(Jan 2016).

The following very high and high critical limiting factors to Cowichan Chinook productivity were identified in 2013 and updated in 2016 (Table 1).

A full detailed list of the critical limiting factors can be found Cowichan Risk Assessment Workshop Jan 29th, 2016.

Cowichan River Hydrology and Critical Limiting Factors

Many of the factors limiting Cowichan Chinook production are related to or exasperated by low flows in the Cowichan River. Adequate flow, as well as water temperature, in the river is key to timing of fall Chinook migration up-stream from the estuary. Spring run fish are more acutely challenged by these issues as they try and migrate up in very low flows and near lethal temperatures. In recent years, Chinook have been delayed by long summer drought conditions lasting well into the fall and water storage in the lake has not allowed for pulse flows to help migrating Chinook get up the river.

Table 1: Cowichan Chinook Critical Limiting Factors to Productivty in Freshwater(2016)

Life Stage	Risk Factor Category	Watershed Health Goal	Explanation
Adults	Very High	Hydrology and Biological Communities	Low water in late summer and early fall is preventing or delaying chinook migration through the lower river which makes them extremely vulnerable to seal predation in the estuary and lower river. (LF1)
Fry-smolt	Very High	Physical Habitat	Lack of high quality rearing habitat ie natural instream complexity (deep >1m holding pools, functional LWD, boulder cover, riparian cover) in mainstem and side channels (LF25)
Egg-smolt	Very High	Physical Habitat	There is a significant lack of off-channel habitat in the lower river, mainly due to loss of access to historical tributary and off channel habitat (LF23)
Egg-smolt	Very High	Physical Habitat	There is a lack of good quality estuarine and nearshore habitat, whether through loss of the habitat or loss of access. The estuary and the lower river are linked; chinook salmon likely move between the two several times. The lack of connectivity between the north and south side of the estuary, due to development and road building was specifically identified as an issue. (LF 31)
Fry-smolt	Very High	Biological Communities	Predation of eggs, alevins, fry, smolts in the middle and upper reaches of the river by predators such as birds (eg. merganser), fish (eg. brown trout), and to a lesser extent mammals (eg. bears). (LF18)
Adults	High	Hydrology and Physical Habitat	Under low flow conditions, aggradation creates a migration barrier in the lower Cowichan mainstem during summer and early fall period. (LF4)
Adults	High	Hydrology	Under low flow conditions upstream migration of adults through the lower and middle reaches of the river is being impeded. Spawners may not reach the spawning grounds or are subjected to stress (eg. high water temperature) which impact spawning capacity. (LF2)
Adults	High	Physical Habitat	Loss of safe migration route through the lower mainstem Cowichan River due to channelization, loss of habitat complexity and instream cover features. (LF3)

Marine Survival - Chinook salmon spend much of their lives in the marine environment where exposure to many different factors affects survival. While mortality occurs throughout the marine residency, mortality in the first year of ocean entry is considered to be a substantial contributor to the strength of return for any year class (Peterman 1987; Beamish and Mahnken 2001). Duffy and Beauchamp (2009) attribute recent declines in survival of Puget Sound Chinook salmon to reduced quality of feeding and growing conditions in the early marine residency.

Prior to 1990 the average survival to age 2 was approximately 5%. A precipitous decline occurred for ECVI chinook in the early 1990s to less than 1%. Within the suite of ECVI chinook indicators there is a marked increase in the survival of Cowichan chinook starting in about 2009 brood year (went to the ocean in 2010); from about 0.5% survival to as high as 2%^[7]. The most recent drop in survival in 2012 and 2013 is likely due to incomplete data. Only data through 2015 returns were available for this analysis. Updates will be available by April 2017.

Recent work on the Cowichan, using PIT tags, provided additional insight into sources of mortality during migration downstream from the release site in the upper river. During years of low spring flows upwards of 90% of the hatchery release did not arrive at the lower river. This freshwater mortality factor is included in the estimate of survival for release to age 2 pre-fishery recruit shown in these graphs.

Climate Change - Climate change will affect both freshwater and marine environments with the ongoing gradual increase in surface air, freshwater and sea surface temperatures anticipated. Implications of climate change on salmon can occur through various life stages. For example, climate change can affect bioenergetics as well as create low flow barriers or reduced spawning habitat availability during migration and spawning (Hyatt 2013). As well, an increase in water temperature could result an increased rate of incubation and an earlier emergence timing that could potentially affect alevin and fry survival. Marine physical and biological oceanographic conditions, including timing of phytoplankton blooms and subsequent secondary production affect the growth and survival during the initial marine residency period.

Fisheries - As a stock of concern, actions have been taken to reduce fishery related impacts that were near 90% prior to the decline of the early 1990s. However, among Strait of Georgia chinook indicators, Cowichan chinook consistently appear to have a higher exploitation rate. Coded Wire Tags (CWT) can provide estimates of fishing mortality. Estimated total mortality (also called exploitation rate) includes reported catch plus release mortalities. The annual total exploitation rate (ER) from Coded Wire Tag recoveries is presented in Figure 9 which indicates that the recent 6 year average exploitation rate is in the order of 60% from all fisheries. That 60% exploitation is distributed among fisheries shown in Figure 10. The Strait of Georgia sport (GST sport) is the fishery with the greatest impact on Cowichan chinook.

Acceptable levels of exploitation depend on the productivity of the stock that is often defined as the average number of recruits produced by each spawner. Based on average productivity across all years the optimum exploitation rate would be in the order of 70%. However, as experienced from 1995-2006, during a period of declining productivity, continuing with a 70% harvest rate increased the rate of decline. If we assume productivity was half of the long-term average then exploitation should have been reduced to a level in the order of 45% to sustain the stock levels. These benchmarks bound discussion on the appropriate exploitation rate. Natural mortality estimates, in relation to marine productivity, are also currently under review (SBC Chinook SPI 2016 Draft).

Figure 10: Distribution of Exploitation on Cowichan Chinook.

Hatchery Supplementation Risks - The Cowichan River hatchery production may also have the potential to negatively impact natural production through competition for food and habitat, disease transfer, genetic introgression, etc. Some concerns exist that hatchery production is causing lower natural recruitment. DFO and other partners are reviewing these concerns in more detail. However, it is generally held that changes in the Strait of Georgia marine conditions resulted in a period of low productivity for most salmon stocks in the area from about 1990 through 2006. There is no evidence at this time that hatchery production contributed to that decline in productivity.

Action Plan For Rebuilding Cowichan Chinook

The Cowichan Watershed Health and Chinook Initiative, is the foundation for a collective and integrated management effort focused on Chinook abundance and supporting robust fish stocks in a healthy watershed.

In order to maximize chinook productivity in fresh and salt-water environments, efforts in harvest management, hatchery supplementation, research and monitoring and education and public outreach will be required. The Cowichan Chinook Initiative is based on current research about the relationships between watershed processes, land-use and fresh-water habitats affecting watershed health. Marine influences, including climate change, oceanic influences and marine fish harvest are also considered.

Each of the key watershed health attributes establishes and describes goals the strategy is trying to achieve. Recommended Actions describe efforts to be made by interested parties, aimed at achieving Initiative goals and, thereby, increase the likelihood of more robust chinook populations in the Cowichan River system over time.

Focusing on achieving these goals will focus on maximizing returns and spawning success while also allowing healthy, robust smolts entering the estuary a much better chance of surviving challenges they will face in the ocean. Ensuring chinook abundance will require a focus on decreasing mortality or critical limiting factors in fresh-water. The Chinook Initiative describes a recommended series of actions that, if taken, are likely to increase the number of returning adults and the survival of their offspring, and thereby continue to re-build Cowichan chinook populations into the future (Figure 10). Detailed action plans proposed for each Critical Limiting Factor can be found summarized later in this document or in detail at the following hyperlink here.

Cowichan Chinook Vision

The Vision Statement for Cowichan Chinook is described as A healthy, spatially diverse return, in timing and distribution, of spring-summer and fall timed chinook adults to the spawning grounds, with enough to support vibrant Cowichan Tribes and other fisheries.

The current DFO escapement goal for Cowichan fall chinook is 6,500. In times of low marine survival the Cowichan Recovery Plan proposes the escapement goal should be 8,000 for spawning and 4,000 for hatchery broodstock. An escapement goal for spring run chinook has not been set.

Proposed management actions were categorized to address both watershed health pressures or threats and chinook limiting factors directly or indirectly in the river, estuary and marine environments, and will require technical and management review. The actions are proposed as a starting point, where re-building Cowichan chinook stocks is a collaborative focus to achieve watershed health as a means to address chinook production, providing a win-win all around.

Management actions will be prioritized based on:

Benefit to watershed health goals and/or mitigation of chinook critical limiting factors.
Available resources and funding.
a champion to lead the action.

An implementation strategy is proposed below.

Freshwater Habitat Health Actions

Actions to improve watershed and habitat health may flow out of larger scale programs, plans, acts, policies, and regulations, such as:

Sustainable Forest Management Plans include hydrological assessments and riparian protection, large-woody debris recruitment etc.
Local government land-use and infrastructure plans
Transportation and infrastructure plans
Cowichan River Parks Plan
Riparian Area Regulation
Fisheries Act
Cowichan Estuary Management Plan
Cowichan Tribe Land-use and Community Plans
Forest and Range Practices Act
Riparian Areas Protection Act

Specific actions will generally be small scale site-specific or project-level actions aimed at enhancement and restoration of key and critical habitats; near-stream and floodplain management actions; and conservation easements and willing seller park additions. These are summarized below. Detailed actions related to each Watershed Goal and Critical Limiting Factor can be found in the summary table or in the 2-page action plans appended to this report.

Habitat Protection, Restoration or Enhancement Actions The Cowichan Watershed is large and complex and attributes such as physical habitat and hydrology have been influenced greatly due to land-use and climate change. The CVRD, Cowichan Tribes and other levels of government have been focused on understanding these changes. Hydrological models have been developed for the watershed but still remain un-tested and much is in flux around our state of knowledge of the watershed and its attributes or future climate influences. Broad-scale hydrologic restoration projects will require additional information such as:

Additional lake water storage needs to buffer climate change impacts
Forest hydrology impact studies
Assessing ground-water resources, influences on Cowichan and Koksilah river flows and understanding supply and demand metrics

The Cowichan River and salmon have been a focus for many studies over the years. This wealth of knowledge provides a good basis for action. A summary of recommendations from habitat and specific chinook research can be found here. In addition, some key habitat restoration projects have been completed in the Cowichan to date (a complete list can be found here).

Other recommended riparian restoration and protection projects include:

Digitizing maps from the year 1890 on to review and quantify true changes in riparian systems on the Cowichan and Koksilah rivers
Conducting riparian assessments and engaging in restoration planning for the Lower Cowichan River
Working with the Cowichan Diking Authority to restore and re-plant riparian edge environments
Conducting an Invasive Species Inventory and organizing efforts for their removal
Including riparian protection strategies in land-use plans for Cowichan Tribes and local governments.

Other recommended riverline restoration and protection projects include:

Providing adequate in-stream large wood debris (LWD)
Assessing critical habitat including estuary, in-river pools, riffles and LWD and restoring habitat complexity and estuary cover
Providing access to historical off-channel habitat, especially in the lower river
Managing accumulated sediments in lower river (follow CVRD Sediment Management Plan)
Assessing and restoring spawning habitat in upper river and Cowichan Lake tributaries

Near stream and flood plain management Detailed actions for the near-stream zone around the Cowichan and Koksilah will be available upon completion of the Cowichan/Koksilah Chinook Critical Habitat Inventory being conducted by Cowichan Tribes. The Cowichan/Koksilah Integrated Flood Management Plan and subsequent sediment management plan outlines many actions related to restoration of the flood plain.

Conservation Easements and 'Willing Seller' Park Additions - Local governments are encouraged to prioritize retention of riparian and key hydrological areas as either conservation easements or park additions. The Cowichan Valley Land Trust and other environmental non-government organizations are encouraged to work with land-owners to establish conservation easements and a stewardship ethic on their own properties.

Predation Management Actions

Managers and interest groups know that adult and fry predation is ranked as a very high critical limiting factor to supporting robust Cowichan River Chinook populations. However, a breadth of knowledge is still needed in-terms of understanding the full impact of predation on Cowichan Chinook in the river and estuary environments.

Pinnepeds in the estuary and the lower river are thought to target adult Chinook, especially females, during staging before migrating up the river and as smolts enter the estuary. Key actions required to understand, quantify and minimize predation by other carnivorous marine mammals include:

Conducting/Updating a Chinook Habitat Assessment in the Cowichan Estuary
Quantifying the number and predation rate of pinnepeds on adult and juvenile Chinook (Cowichan Tribes estuary predation project; UBC Marine Mammal Lab research in the Strait of Georgia; Salish Sea Marine Survival Project)
Assess and engage stakeholders to manage and minimize the impacts of log booms in the estuary.

Predation of eggs, fry and smolts by fish, amphibians and birds is also being studied in the Cowichan River that will provide a sense of natural losses that occur in the riverine ecosystem.

Proposed:

Complete the Brown Trout Predation Study in the Cowichan River

Fisheries Management Actions

Cowichan chinook are distributed throughout southern BC and into Washington State. The annual distribution varies, likely based on marine conditions, food availability, etc.. The following actions have been implemented in ocean fisheries to reduce impact on Cowichan chinook, including:

Size limit restriction in the Strait of Georgia recreational fishery
Approximately 50% reduction to the WCVI commercial troll fishery for chinook
Spot closures throughout the northern Strait of Georgia recreational fishery
size and daily limit restriction from March to July in the Victoria area and southern Strait
a terminal area 'Gulf Islands' closure extending from Nanaimo down to Saanich during August-October

At this time there are no management actions specific to red, amber, or green status zones as described in the Wild Salmon Policy. These actions apply to all status levels.

Cowichan Tribes have unilaterally reduced take for food and ceremonial (FSC) purposes during periods of low water and concern for chinook migration. Other fisheries within the Cowichan Bay and river are managed under the auspices of the Cowichan Harvest Roundtable.

Future fishery management actions will be informed and influenced by strategies developed as part of the Southern BC Chinook Strategic Planning Initiative (SPI). The Cowichan Chinook stocks are included within this initiative.

Hatchery Supplementation Actions

The Cowichan River Hatchery has been operated by the Cowichan Tribes under contract to Fisheries and Oceans Canada (DFO) as part of the Salmonid Enhancement Program (SEP) since 1978. Within the SEP Community Economic Development Program (CEDP) the hatchery was initially established to achieve a range of objectives that included salmon enhancement, providing employment, obtaining stock information, contributing to the local economy, and improving relations between the Federal government and the Cowichan Tribes. The Cowichan River Hatchery has the objective to support re-building of Cowichan Chinook and assessment as an indicator stock for the Pacific Salmon Treaty.

DFO guidance on the hatchery operations which have the objective of rebuilding or maintaining natural stocks is to:

Limit broodstock collection to less than 30% of the returning spawners. The current hatchery egg target is 700,000 chinook eggs. This target has been reduced from over 3M in the early 1990s to ensure SEP guidance is being followed. Over the full period, the 30% guide for broodstock collection was exceeded 6 out of 29 years (21%) presented in Figure 5. One of those years, 2008, was near 50% removal due to the extremely low run size. Over the most recent 5 years, on average less than 10% of the total spawners (natural spawners plus hatchery brood) were removed for brood stock.
Limit hatchery returns to less than 50% of the return. The percent contribution of hatchery origin chinook to the chinook natural spawners has averaged about 29% of the annual return.

Figure 12: Contribution of hatchery origin chinook to natural spawn.

The question arises as to the degree to which hatchery production benefits the river spawners. The following graph indicates that there is considerable variability in the hatchery returns. About 80% of the time the returns were equal to or more than the numbers taken for brood stock. On average hatchery returns are about 46% greater than the broodstock taken.

Figure 13: Results of Enhancement of Cowichan Chinook.

Proposed actions involving the Hatchery include:

Continue to adhere to DFO Fish Enhancement Guidelines (no more than 30% of an expected annual return of fish shall be captured from the river for the hatchery and no more than 50% of the return shall be of hatchery origin)
Work towards improved fish homing using river water
Test and refine fry release strategies to improve survival rates
Passive Intregrated Transponder (PIT) Tagging Studies to monitor release strategy success and gather information on life stage mortality

Research and Monitoring Actions

Research: The following key knowledge gaps were identified during the Critical Limiting Factors Expert reviews in 2013 and 2016:

Lack of knowledge regarding the available food supply and rearing capacity in the Cowichan Estuary as well as identification of key and critical habitat to protect and restore for Chinook production
Quantify the amount of aquatic rearing habitat that has been lost in the lower river over time
Estimations of annual freshwater juvenile production on an annual basis for fall Chinook (egg to fry survival, fry to smolt survival and hatchery effectiveness) to determine how many wild and hatchery Chinook are currently entering the marine environment. This was also highlighted as an important action item and assessment tool in the 2005 Cowichan Recovery Plan (LGL 2005)
Lack of information and focus on the spring Chinook run in the Cowichan River, including genetic distinctness, distribution in the watershed, current abundance key migration period and rebuilding potential
Lack of information regarding the existing and potential use of the Koksilah River by Chinook
Uncertainty of the density dependent effects of large hatchery releases of Chinook fry on the survival rates of wild raised Chinook fry
Increase understanding of threats and limiting factors affecting juvenile survival in estuary and early marine habitats, especially in the Strait of Georgia and WCVI, and mitigate these factors where possible (link to Southern BC Chinook Strategic Planning Initiative)
Uncertainty on the impacts of aquatic invasive plant species to fish access, cover rearing and passage, including invasive plants in riparian areas
Some of the CLFs that affect fall run Chinook likely impact early run Chinook as much or even more: for example, low summer flows, woody debris, gravel, log jams, water temperature, etc.
What flows are required to allow for appropriate sewage dilution
2014 and 2015 were very different years but there were still large numbers of fish in the bay. It would be useful to see how fish behave with each incremental drop in flows
What accounts for the high level of in-river juvenile mortality as evidenced by the BCCF PIT tagging studies and DFO’s Rotary Screw Trap Studies

Monitoring

Review of Critical Limiting Factors every 2 years
Update knowledge gaps filled each year
Partners to review action items, update based on critical factors review and prioritize

Education and Outreach Actions

Best Management Practices a number of BMPs exist for local government, developers and citizens for protecting fish and fish habitat.

Create a list of BMPs that are easily accessible for planners and citizens

Cowichan Watershed Health & Chinook Initiative

Cowichan Watershed Health

And Chinook Initiative