Moorings, Remote Sensing, and Ferry Sampling

There are three key projects under this category.

1. Continuous phytoplankton monitoring in the Strait of Georgia

Team: Stephanie King, Sea This Consulting

Changes in abundance of nutrients and phytoplankton as well as changes in the timing of the spring bloom can potentially impact populations of coho and Chinook. In order to properly monitor the variability of the rapidly varying phytoplankton biomass, continuous measurements in the near surface of the Strait are necessary. The two existing Strait of Georgia weather buoys (Halibut Bank, 49° 20.4′ N  123° 43.6′ W, and Sentry Shoal, 49° 54.4′ N  124° 59.1′ W ) offer convenient platforms for such measurements.  Fluorometers measuring surface chlorophyll fluorescence, turbidity and temperature have been deployed on these two buoys in the central and northern Strait of Georgia. Additionally, chlorophyll fluorescence is being monitored near Egmont, where seeding from coastal inlets has been linked to early spring blooms. The data collected will provide a high temporal resolution time series describing relative bloom concentration and timing. The team also plan to process satellite imagery for chlorophyll and fluorescence line height (FLH) from February to May to provide spatial context for the spring bloom.

In addition, Canada’s Ocean Network (located at UVic) has successfully instrumented two of the BC Ferries that transit the Strait of Georgia daily.  The crossing from Tsawwassen to Swartz Bay (currently being installed) and from Tsawwassen to Duke Point (Nanaimo) will record surface oceanographic parameters continuously.  In collaboration with the Ocean Network, the SSMSP is investigating also equipping the Comox to Powell River ferry.  The latter would provide an important continuous measure of surface oceanographic parameters in the central basin of the Strait of Georgia.  Further, the SSMSP will assist with the monitoring and maintenance of this equipment.


To provide data that can be used by ecosystem scientists and modelers to describe bottom-up processes impacting juvenile salmon.


Phytoplankton bloom timing and concentration is a major driver of the marine ecosystem and potentially one of the keys to understanding the growth and survival of juvenile salmon in the Salish Sea.  High temporal resolution time series are required to adequately characterize phytoplankton variability and explain how blooms impact food availability for salmon.

King and her team are continuously monitor phytoplankton for three years (2015-2017) using fluorometers deployed at three locations in the Salish Sea. Sampling locations are at three locations as shown in Figure 1 and will provide data in the relatively data-poor central and northern parts of the Strait of Georgia (Halibut Bank, Sentry Shoal), as well as at the mouth of a coastal inlet (Egmont). Two additional sensors have been deployed on the Sentry Shoal Buoy: SBE-37 MicroCAT, a temperature and conductivity sensor and the Satlantic SUNA V2, an optical nitrate sensor.  Both have been deployed at the surface to provide a continuous time series of temperature, salinity and nitrate from April 2015.

The fluorescence time series builds on data collected as part of the Fisheries and Ocean’s Strait of Georgia Ecosystem Research Initiative (ERI) during which fluorometers were deployed at Halibut Bank and Egmont.

The buoy monitoring program supports testing several of the SSMSP key hypotheses relating to prey availability, productivity and the health of the ecosystem.  The high temporal resolution dataset is complementary to the periodic sampling done by SSMSP Citizen Science monitoring and DFO surveys.

Figure 1. The three sampling sites for chlorophyll fluorescence time series in the Salish Sea


Oceanographic sensors were deployed and maintained in 2015 until the present at Halibut Bank and Sentry Shoal, and in the spring at Egmont.  High temporal resolution time series were collected for chlorophyll fluorescence, turbidity, temperature, salinity and nitrate.  The SSMSP project initiated monitoring at Sentry Shoal and extended the time series at Halibut Bank and Egmont which now run from 2011 to 2016 and 2010 to 2016, respectively.

Key results from the monitoring include:

1) The buoy data can be used to describe the timing and magnitude of the spring bloom in the northern (waters to the northwest of the center of Texada Island) and central (waters from the center of Texada to 49oN) Strait in 2015 and 2016

2) Buoy data and satellite data confirm seeding from inlets in 2015.

3) There is a correlation between seeding from inlets and an early spring bloom (by ~1 month, 2003 to 2016)

4) The in situ chlorophyll fluorescence data and satellite FLH agree

5) The spring bloom in the central Strait is 5 days earlier on average compared to in the north

6) The SUNA nitrate sensor is an exciting new instrument for monitoring Nitrate concentration autonomously and is an important factor in informing phytoplankton bloom timing

7) A very unusual, bright, coccolithophore bloom was observed in 2016 in satellite imagery and in the turbidity time series at Halibut Bank

At Halibut Bank, time series for chlorophyll fluorescence, turbidity and temperature have been maintained since January 2011 (Figure 1).  The quality and consistency in the dataset improved with the SSMSP funding starting in 2015 which allowed more frequent servicing trips and calibration.  At Sentry Shoal, chlorophyll fluorescence, turbidity and temperature have been measured since 2015.  This is the first high temporal resolution time series of surface conditions in the northern Strait, and the first high resolution time series of Nitrate in the Salish Sea (Figure 3).  At Egmont, chlorophyll fluorescence has been monitored in the spring each year since 2010 to monitor potential seeding from inlets.  In 2015, satellite imagery and buoy data confirmed seeding from Desolation Sound triggering a very early spring bloom in the northern Salish Sea on Feb. 21, and seeding from Howe Sound and Jervis Inlet initiating the bloom in the central Salish Sea on March 7 (Figure 4).

Figure 2.  Annual surface chlorophyll fluorescence at Halibut Bank from 2011 (top) to 2016 (bottom).  In 2013 and 2015 there was an early spring bloom.  In 2015 the spring bloom was early with very high concentrations compared to other years.  In 2016 the spring bloom timing was average, but low in magnitude.  Concentrations were lower than normal in 2016 until a large bloom in late August.

Figure 3. Nitrate time series (black) in 2015 (top) and 2016 (bottom) at Sentry Shoal.  The vertical blue dashed lines show when the sensor was cleaned and/or calibrated.  Note that calibrations were done with dionized water, but the data have not been compared to any in situ samples yet

Figure 4.  MODIS Fluorescence Line Height (FLH) image series from late February to early March 2015 shows early blooms in Desolation Sound, Sechelt Inlet and Howe Sound seeing followed by an early bloom in the Strait of Georgia.  Sensors at Sentry Shoal (top plot) and Halibut Bank (bottom plot) confirm the bloom start dates of Feb. 21 and Mar. 7, respectively.  The fluorometer at Egmont (middle plot) measured increased chlorophyll about 5 days before the spring bloom in the central Salish Sea.

Fluorescence Line Height (FLH) from NASA’s Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Aqua satellite was processed to provide spatial context for in situ measurements.  FLH has a linear relationship with chlorophyll at concentrations below about 20 mg/m3 and tends to perform better than the standard satellite chlorophyll products, with less confusing signal from aerosols, sediment and dissolved organic matter.  Satellite imagery is useful for looking at spatial variability in blooms and has been used to establish a correlation between seeding from inlets and an early spring bloom in the Strait of Georgia.  Seeding was observed in satellite imagery from 2004, 2005, 2007, 2008, 2009, 2013 and 2013.  In years with no seeding (2003, 2006, 2010, 2011, 2012, 2014 and 2016) the bloom is later by about one month.  Satellite imagery was also used to assess the difference in timing between the northern and central Salish Sea. The bloom is start date is 5 days earlier on average in the southern Strait compared to the northern Strait.  There were only two years when the northern Strait was earlier than the southern Strait (2001 and 2015).

A very unusual coccolithophore bloom was observed in the Halibut Bank buoy data and satellite imagery in August 2016 (Figure 5).  There are no other records of this type of event in the Strait of Georgia in recent years.

Figure 5.  MODIS true colour imagery from NASA’s Worldview (; top) show a coccolithophore bloom with the peak brightness on Aug. 22, 2016.  The bloom lingered in inlets into September. The plots show the turbidity time series at Halibut Bank from 2011 to 2016.  The largest signal in the time series is in August 2016 from the bloom.

Lessons learned include the following:

  • Autonomous deployments are an effective method for monitoring surface conditions in the Strait. Fouling is a problem but can be mitigated with anti-fouling measures such as copper and shorter deployments during periods of high growth.
  • The new SUNA nitrate sensor gives promising results and can be linked to bloom timing in the summer. Having multiple sensors at one site allows events to be explained in more detail.  For example, a bloom in early August was initiated by a wind driven mixing event which mixed nitrate to the surface.

Figure 6.  A strong and persistent north-northwest wind from July 26 to 31 (lower plot) initiated mixing as initiated by the decreased temperatures, increased salinity and increased nitrate (middle plot).  The peak nitrate, reaching concentrations near to winter conditions, was followed by a plankton bloom several days later (top plot).   Note the daily decrease in chlorophyll fluorescence from non-photochemical quenching.  Times are in UTC.  Wind data are averaged from the buoy data available on

High resolution measurements are needed to accurately characterize the ephemeral nature of conditions in the Strait.  Furthermore, adding the northern monitoring site at Sentry Shoal in 2015 has demonstrated variability between different areas of the Strait.  The time series at Halibut Bank and Egmont are now over 6 years in length and can be used to explain interannual variability that may be linked to juvenile salmon survival.  For example, observations such as the very late spring bloom in 2011 or the relatively low biomass in 2016 may indicate unfavorable conditions for juvenile salmon entering the Strait.

The monitoring at the three locations will continue into 2017 and hopefully beyond.  At Sentry Shoal, an exciting new collaboration with the Hakai Institute began in summer 2016 with the deployment of a SeaFET pH sensor on the Sentry Shoal buoy.  Wiley Evens, Hakai will take over the field deployments in 2017 at the northern site with fluorometer support by Sea This Consulting.  Sea This will maintain the sensors at the other locations.

2.      Use of sediment traps and moored instrument arrays to determine bottom-up controls in the Strait of Georgia

Team:  S. Johannessen, R. Macdonald,& R. Thomson (DFO/IOS- Sidney)


The ultimate aim of this project is to relate juvenile fish health and survival to the timing and extent of blooms and ultimately to the physical forcing that drives the productivity.Specifically, this project will analyze four years of existing geochemical samples and data from the northern Strait to assist in the development of a quantitative description of the relationship between timing and relative magnitude of phytoplankton and zooplankton blooms, as compared with marine survival of juvenile fish during the same period.


The survival of juvenile salmon during their first year in marine waters may be strongly affected by the quality, quantity and timing of food available in the Strait of Georgia.  Sophie Johannessen’s team wish to develop an indicator that links physical conditions (stratification, circulation, winds) with the timing and magnitude of phytoplankton blooms, the response by zooplankton, and the health of juvenile salmon.

This project addresses the primary objective of the Salish Sea Marine Survival Project, “to identify the most significant factors affecting marine survival of juvenile salmon in the Salish Sea marine environment.”  Following the 2013 workshop, the SSMSP Advisory Panel concluded that “food supply (including the quantity, quality, timing, and spatial extent of prey and the impact of competition on food availability) was considered the strongest likely mediator of size and growth,” and particularly encouraged projects that addressed the hypothesis of bottom-up control of juvenile salmon survival.  This project addresses that hypothesis directly by assessing the relative quantity, quality and timing of food available to juvenile salmon and later comparing that assessment with health indicators of juvenile fish caught during the same season. Sediment traps collect particles that provide a record of biological and geochemical processes in the upper water column that augments periodic sampling cruises, and spans the time between such cruises.  For example, short-lived events like blooms will be caught in the sedimenting material, even if missed by ship-based sampling, and the quality of the sedimenting material informs us about what caused the bloom, and how large it was.

Past data have been collected from sediment traps placed on a mooring in the northern Strait of Georgia, providing a continuous record of sinking particles. A Baker sediment trap has been deployed at 50 m in the Northern Strait of Georgia to collect sinking particles continuously throughout the year.  The location of this mooring is the site of an existing four-year time series (2008- 2012). The samples will be analyzed for dry weight flux and organic composition ( organic C, N, biogenic Si, stable isotopes of C and N) at the University of British Columbia, following procedures consistent with previous work (Johannessen et al., 2005; Sutton et al., 2013).  The proportion of bloom-type and non-bloom-type organic matter will be interpreted from the stable isotopes (Johannessen et al., 2005) and combined with the biogenic silica, organic C and N data and the chlorophyll fluorescence of the sinking material to provide a picture of the timing and relative magnitude of the export of phytoplankton blooms.  Taxonomist Dr. Lou Hobson will identify phytoplankton with reference to published collections (Hobson, 2009) and enumerate zooplankton fecal pellets.

If successful, the number of moorings, and associated sensors, may be increased in the future, and studies will be developed to also relate ocean circulation and stratification and associated meteorological conditions (winds and cloud cover) with the timing and extent of blooms. The ultimate aim of this project is to relate juvenile fish health and survival to the timing and extent of blooms and ultimately to the physical forcing that drives the productivity.

Some of the key questions that are being addressed are:

-How do the timing, frequency and composition of phytoplankton blooms vary from year to year
-Which kinds of phytoplankton blooms result in large zooplankton blooms?
-How do the chemical and biological composition of the sinking material relate to the type of bloom?
-How does juvenile salmon survival relate to the timing and composition of blooms in the same season?


This study began in summer 2016 and is in progress. By the end of the fiscal year (April 2017), they will have a time series of phytoplankton and relative zooplankton biomass (inferred from fecal pellets) in the northern Strait of Georgia for 2008 – 2014 that can be combined with their existing time series of the chemical composition of sinking organic matter.  From these data, they will assess the timing and quality of food for zooplankton and hence for juvenile salmon.  They will compare the sediment trap record of food availability with indicators of juvenile salmon health as reported by the salmon group at the Pacific Biological Station and St. Andrew’s Research Station (Marc Trudel, Rusty Sweeting).

Possible next steps include the following:

  • If they find a strong link between the timing of available food and the health of the outmigrating smolts, that will indicate a strong bottom-up control on survival. If timing turns out to be critical, then a possible next step would be to change the timing of the release of hatchery-raised smolts. Smolts could be released at staggered times, with tags linked to release date, so that the survival rate of smolts released at different times could be assessed.
  • If this study shows a weak link with the health of smolts, or if the link seems to be present in some years but not in others, that result would support the hypothesis that, since the main population decline in the 1970s, the number of coho and chinook salmon has been so low that the fish are vulnerable to every stressor. Preliminary results from other project support this hypothesis.  If that is the case, then a possible management response would be to reduce all the stressors within local control (low river discharge during outmigration or return, contaminant discharge into rivers, habitat destruction, fishing, releasing juveniles from hatcheries too early to catch the main biomass peak of zooplankton). This would give the fish a better chance to be resilient to long-term climate change and to recover from the rapid decline in the 1970s.
  • This activity will be associated with juvenile salmon studies, once their time series is complete. The other collaborators (Marc Trudel, Rusty Sweeting) are still willing to carry out the collaborative work. The jellyfish time series collected incidentally as part of this project might turn out to be useful too.  They intend to pursue a collaboration with fisheries and zooplankton researchers to determine whether amphipods associated with jellyfish might provide food for juvenile salmon and explain some of the variability in their survival (idea proposed by Dick Beamish).

3.      Remote Sensing

Team: Maycira Costa UVic, Akash Sastri ONC, Lyse Godbout DFO, Justin Dell Beluz, Tyson Carswell

Coastal oceans are highly dynamic and of great biogeochemical, ecological, and economic importance. Economically, coastal oceans concentrate marine resources that are increasingly in demand, thus requiring increasing monitoring and managing of these regions. To succeed in these tasks, approaches that provide information at various time and spatial scales are needed, which must involve a degree of both continuous and sustained data collection.

One temporally and spatially dynamic coastal system under strong influence of terrestrial and oceanic inputs is the Salish Sea.  The goal of this project is to determine the spatial-temporal dynamics of Salish Sea in the last fifteen years using remote sensing and data acquired from vessels of opportunities (BC Ferry – FOCOS and FeryBox, Ricker, and citizen science boats) to test hypotheses on spatial and time domain fluctuations in the phytoplankton bloom phenology (timing, duration, and amplitude) and water turbidity and environmental physical drivers. Bloom phenology and turbidity from the different geographical domains in the Salish Sea and fisheries indices will also be explored in collaboration with fisheries biologists from PBS.


The goal of this project is to determine the spatial-temporal dynamics of Salish Sea in the last fifteen years using remote sensing and data acquired from vessels of opportunities to test hypotheses on spatial and time domain fluctuations in the phytoplankton bloom phenology (timing, duration, and amplitude) and water turbidity and environmental physical drivers.


SSMSP is utilizing a number of different approaches to examine bottom-up processes, including those that provide information at various time and spatial scales. Satellites, radiometers, and other optical sensors aboard of vessels of opportunity and buoys can allow for continuous and sustained data collection. Operational ocean colour satellites such as MODIS-Aqua and the upcoming Sentinel-3 provide a great opportunity for continuous data acquisition at high temporal resolution, and provide the data required for a long-term monitoring program in the Salish Sea.

Maycira Costa is addressing specific knowledge gaps in spatial-temporal biogeochemistry of the Salish Sea by using synergistic methods that include (i) ocean colour satellite imagery, (ii) sensors aboard vessels of opportunity (FerryBox and FOCOS-BC Ferries), (iii) in situ data from research cruises, and (iv) in situ data collected from citizen science boats. A fifteen year remote sensing data set will allow her group to analyze the spatial-temporal phytoplankton bloom phenology of the Salish Sea in relationship to environmental time series data (SST, Fraser discharge, turbidity, wind, light availability) and global climate indices.

This project will allow the researchers to contribute to one of the primary objectives of the Salish Sea Marine Survival Project (SSMSP), which is to determine if thebottom-up processes driven by annual environmental conditions are the primary determinate of salmon production via early marine survival”. The proposal will also contribute to the “trend analysis and modeling” component of the SSMS project by providing spatial temporal data that can be used to initiate and/or provide parameterization for the models.


This project was initiated Fall 2015 and time-series imagery analysis is ongoing.  An NSERC USRA student is working on the data-integration component of the project. Data has been compiled from a number of different sources, and Costa et al are defining a method to evaluate and pre-define spatial-temporal biogeochemical provinces in the Salish Sea.  The data being analysed include spatial temporal Chla data from (1) ONC ferrybox systems aboard the BC Ferries, (2) the Institute of Ocean Sciences (IOS) public database, (3) Dr. Ian Perry data collected every two weeks as part of the PSF project, (4) Citizen Science Project (boats) data collected in 2015 and 2016, (5) Svetlana Esenkulova microscopy data Feb-Oct biweekly, ~1300 samples for 2015 and daily 2016, (6) buoy data acquired by Stephanie King.

The time-series of satellite imagery (2002-2016) has allowed for the understanding of the phytoplankton dynamics in the Salish Sea with an annual characterized spring bloom generally occurring at the end of March in the Central Salish Sea and middle of March in the North Salish Sea, except in 2005 and 2015 when the bloom happened two month earlier. The spring bloom is generally followed by a lower magnitude late summer or fall bloom. Specifically, this work addresses the general hypothesis that the size of the salmon return is, to some extent, related to the time of juvenile marine entry and the time of the zooplankton bloom and its related phytoplankton bloom.

  • Objective 1: Derive fifteen years of spatial-temporal improved biogeochemical based on present MODIS – available since 2002 and Sentinel-3 (available since June 2016) ocean colour satellites.

Progress: Sentinel-3 imagery is in the processing and evaluation phase. Empirical orthogonal function temporal method is applied to the chlorophyll satellite-derived products for better spatial representation of the data. Satellite-derived chlorophyll concentrations and zooplankton data are combine to examine the synchrony of phytoplankton and zooplankton phenology in the North and Central Salish Sea from 2002-2016. This will be part of the foundation data to help improving the accuracy of adult return forecasts

  • Objective 2. Define integration method to use data acquired from vessel of opportunities (BC Ferry/ONC unattended continues FerryBoxes and Ferry ocean Colour Observation Systems – FOCOS unattended continuous above-water reflectance from moving ferries crossing the Salish Sea, and citizen science boats) to calibrate and validate satellite imagery and products.

Progress: FOCOS was installed, tested, and now is operational.  The citizen science program “water colour” was successfully done in the spring and summer as part of the Coastal naturalist program in the Queen of Oak Bay. Data is now under analysis. BC ferries wants to incorporate “water colour” as part of their environmental awareness program in the spring and summer. They would like to add this program to the PSF citizen science boats. All the technology developed in Objective 2 is successfully used in Objective 1.

In summary, the results of this project to date are as follows:

  • Empirical orthogonal function temporal method is applied to the chlorophyll derived products for better spatial representation of the data.
  • Sensors to measure water leaving radiance successfully installed in two BC ferries. The data is used for validation of atmospheric corrected satellite imagery; MODIS and Sentinel-3
  • Chlorophyll climatology (2002-2016) indicates the seasonality in the Central Salish Sea. Bloom initiation on average happens on March 29 (±4 days) and on March 20 (±4 days) for the Central and North Salish Sea, respectively. The chla climatology also indicates that, for both the Central and Northern regions, late summer and fall blooms occur.
  • In 2014, 2015, and 2016, bloom initiation happened on April 2, Feb 21, and March 8 in the Central region, and April 10, Feb 21, and March 16 in the North region. This indicated an early bloom condition in 2015 and 2014, and normal bloom conditions in 2016.
  • Satellite-derived chlorophyll concentrations and zooplankton data are combine to examine the synchrony of phytoplankton and zooplankton phenology in the North and Central Salish Sea from 2002-2016. Initial results indicate relationship between zooplankton abundance anomaly and time of bloom initiation.

A post-doc, Dr. Suchy, in collaboration with Costa and Perry will also focus on investigating the level of synchronicity between phytoplankton and zooplankton phenology in the Salish Sea. Time-series data for phytoplankton from satellite imagery, buoy data, ferry data, citizen science data, and research cruise data will be coupled with historical and present zooplankton data. By looking at long-term spatial data of phytoplankton and zooplankton, they can identify their response to different climate drivers (e.g. SST, wind). Ultimately, changes in the seasonal patterns of these lower trophic levels will provide insight into their influence on the growth, survival, and overall return strength of salmon populations in the region. Karyn began work in July 2016 and is focused on two major objectives:

Objective 1: Examine the synchrony of phytoplankton and zooplankton phenology in the Northern/ Central Salish Sea from 2002-2016 by integrating satellite products with historical and present zooplankton data. Sub-regions of focus: North and central due to optimal; data availability. Environmental drives to be considered: chlorophyll satellite-derived data, zooplankton data (abundance biomass class size, life stages), satellite-derived SST, satellite-derived PAR, Fraser runoff, mixing layer from DFO database, wind data, PDO, NPGO, SOI.

Objective 2 – Examine the influence of local environmental drivers on phytoplankton and zooplankton in the Salish Sea from 2014-2016. Sub-regions of focus: Johnstone Strait, Northern SoG, Baynes Sound (?), Central SoG, Southern SoG, Tidal Mixing, and Juan du Fuca. Environmental drivers: chlorophyll satellite-derived data and citizen science boats, zooplankton data (abundance biomass class size, life stages), satellite-derived SST, satellite-derived PAR, Fraser runoff, mixing layer from DFO database, wind data.

Next steps in this project for 2017 include the following:

  1. Data integration with fish telemetry data: Nathan Furey will work on integration of the chlorophyll-derived satellite data and zooplankton (Perry) with the fish telemetry data.
  2. Satellite-derived data for the UBC model initiative: The satellite data will be an important component of the modeling phase. Data requested for the modeling initiative is from 1998 to present. Costa et al will integrate data from 1998-2002 from the SeaWifs satellite with the present time series.
  3. Data integration with Chrys Neville was discussed and will be fostered in 2017. Ideally a Post-doc student could be supported with PSF and MITACS funds to address this component of data integration.