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

Eagle Eye
Shoreline habitat.

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)

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.

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.

High Risk Assessment

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).

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.

Example of Physical Habitat

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.

Figure 5: Map showing Riparian Condition in Cowichan River Area (LGL, 2005).

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.

Marine Mammal Interactions

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).

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 StageRisk Factor CategoryWatershed Health GoalExplanation
AdultsVery HighHydrology and Biological CommunitiesLow 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-smoltVery HighPhysical HabitatLack 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-smoltVery HighPhysical HabitatThere 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-smoltVery HighPhysical HabitatThere 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-smoltVery HighBiological CommunitiesPredation 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)
AdultsHighHydrology and Physical HabitatUnder low flow conditions, aggradation creates a migration barrier in the lower Cowichan mainstem during summer and early fall period. (LF4)
AdultsHighHydrologyUnder 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)
AdultsHighPhysical HabitatLoss 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.

Figure 8: Percent of Cowichan smolts surviving to age 2.

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.

Figure 9: Total Mortality or Exploitation Rate by catch year of Strait of Georgia Chinook, including Cowichan.

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.

Figure 11: Trend in productivity (R/S) of Cowichan River chinook.


The stewardship community in the Cowichan Watershed is robust and includes all levels of government, environmental and industry leaders (Figure 108). The re-building of Cowichan Chinook stocks is likely to happen only if everyone with an interest in the Cowichan River environment works together. It is proposed that the Cowichan Watershed Board, along with the Technical Advisory Committee take the lead in overseeing implementation of the specific strategies outlined below.

Figure 14: The Cowichan Watershed Stewardship Community.

Cowichan Tribes, Regional Government, Provincial and Federal Government

Strategy – Create a planning committee that provides advice on land-use proposals and plans. This committee would include representation from Cowichan Tribes, planners, environmental staff and engineers from local government and regulatory staff from the provincial Ministry of Environment and the Federal Fisheries and Oceans Canada.

Strategy – Include Chinook Critical Habitat mapping as a layer in planning initiatives. (Note: the Chinook Critical Habitat map is in the works through a Cowichan Tribes mapping project).

Cowichan Watershed Board and Technical Advisory Committee (TAC)

Strategy – Have the CWB adopt the Cowichan Watershed Health and Chinook Initiative as a priority initiative to consider when implementing the Cowichan Basin Water Management Plan.

Strategy – Work with the TAC to implement the key watershed health and habitat actions as part of the Target work plans.


Strategy – Work with Catalyst Paper as a partner in the initiative to address flow issues in the Cowichan River.

Strategy – Work with large forest land owners to minimize impacts to fish habitat and restore hydrological function on their lands.

Ad-hoc Water Forum

Strategy – Incorporate limiting factors relating to flow for Chinook when making in-season water management recommendations.


Strategy – Incorporate the Chinook Critical Habitat map and the list of restoration, education and outreach projects as part of their workplans.

Cowichan Stewardship Roundtable (CSRT)

Strategy – Include regular updates on the progress of the Cowichan Watershed Health and Chinook Initiative at monthly meetings.