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

Results Summary:

Oceanographic sensors were deployed and maintained at Halibut Bank and Sentry Shoal, and in the spring at Egmont for all three years (2015-2017) of the SSMSP program.  Key results from the monitoring program include:

  1. The chlorophyll fluorescence data can be used to describe the timing and magnitude of phytoplankton biomass in the northern and central Strait. In situ measurements and satellite data agree and are summarized in table 1 and as follows:
    • 2015 was an unusual year with a very early spring bloom that started in the north first.  There was higher biomass in the spring and lower biomass through the summer.
    • The spring bloom in 2016 was average in terms of biomass and timing.
    • The start of the spring bloom in 2017 was early in the central Strait and a late in the north. Biomass was similar to 2016.
Table 1. Spring bloom start dates determined from the buoy chlorophyll fluorescence data and satellite imagery.
Northern Strait Central Strait
2015 Feb 18-25 Feb 18-25*
2016 Mar 29-Apr 6 Mar 13-20
2017 Apr 16** Mar 2-8**
* Mar 7 at Halibut Bank buoy

** based on buoy measurement only

  1. There is a correlation between seeding from inlets and an early spring bloom.
  2. The spring bloom in the central Strait is 5 days earlier on average compared to in the north. In 2017 bloom in the north was later by more than a month.
  3. The SUNA nitrate sensor is a new instrument for monitoring nitrate concentration autonomously and has provided the first high temporal resolution record of nitrate in the Strait. Nitrate is an important factor in informing phytoplankton bloom timing.


The buoy monitoring program measured physical, chemical and biological surface properties in the Salish Sea and will give insight into prey availability for salmon as well as describe primary productivity and health of the ecosystem.  High temporal resolution time series were collected for chlorophyll fluorescence, turbidity, temperature, salinity and nitrate.

All objectives of the monitoring project were met.  At Halibut Bank, time series for chlorophyll fluorescence, turbidity and temperature have been maintained since January 2011 (Figure 2).  At Sentry Shoal, chlorophyll fluorescence, turbidity, salinity, nitrate and temperature have been measured since 2015 (Figure 3).  The nitrate and salinity time series were maintained by Sea This Consulting in 2015 and 2016, and by the Hakai Institute in 2017.  Hakai also deployed a SeaFET pH sensor at Sentry Shoal in 2017.  At Egmont, chlorophyll fluorescence has been monitored in the spring each year since 2010 for the purpose of monitoring potential seeding from inlets (Figure 3).

Figure 2. Surface chlorophyll fluorescence at Halibut Bank from 2011 (top) to 2017 (bottom).  In 2013 and 2015 there was an early start to the spring bloom.  Chlorophyll concentrations in spring 2015 were the highest in the spring compared to other years and also compared to the rest of 2015. In 2016 the spring bloom timing was average, but low in magnitude.  In 2017 the there was a very slow start to the spring bloom.


Figure 3. Surface chlorophyll fluorescence at Sentry Shoal from 2015 (top) to 2017 (bottom).  The spring bloom in 2015 was more than a month earlier than in 2016.  In 2017, the spring bloom was very low in biomass.

Figure 4. Surface chlorophyll fluorescence at Egmont from 2010 (top) to 2017 (bottom).  The Egmont time series is used to monitor seeding of the spring bloom from coastal inlets.  Early spring blooms seeded from coastal inlets were observed in 2013 and 2015.  The noise after mid-April is likely due to fouling and will be taken out of the time series.

Lessons Learned:

  • Autonomous deployments are an effective method for monitoring surface conditions in the Strait.  Fouling was a problem in 2015 but was mitigated in 2016 and 2017 with anti-fouling measures such as copper and shorter deployments during periods of high growth.
  • 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 7 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 and 2017 may indicate unfavorable conditions for juvenile salmon entering the Strait in those years.
  • The chlorophyll fluorescence data observed at the buoy is highly complementary to satellite chlorophyll and periodic shipboard measurements.  They worked with the University of Victoria’s SPECTRAL lab, DFO and PSF to assess the different sources of phytoplankton measurements (Figure 5).  The combined results from the phytoplankton monitoring will help researchers understand bottom up drivers of juvenile salmon survival and overall ecosystem health.

Figure 5.  The buoy chlorophyll fluorescence (blue line), satellite chlorophyll (yellow line) and in situ chlorophyll measurements (purple circles) for the northern (top) and central (bottom) Strait.  The pie charts show the species composition from nearby citizen science stations.

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. The spatial and interannual variability of the surface chlorophyll conditions in the Salish Sea can be used as an indicator of primary productivity, and therefore to assess the impact of bottom-up forcing on Chinook and Coho populations. Data derived from satellite remote sensing offer an unparalleled tool for synoptic biomass sampling associated with high sampling frequencies.

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 them 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.

 A post-doc, Dr. Suchy, in collaboration with Costa and Perry is focussing 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. This work began July 2016 after the approval by MITACS.

Outcomes to Date:

  • This project addresses bottom-up processes that will contribute to the understanding of the role of the marine environment on the survival of salmon in the Salish Sea. They present their preliminary analysis on the dynamics of the environmental variables and relationship with the base of the food web in the SS.
  • Results show chlorophyll a was anomalously high in spring 2005 and 2015. Anomalously high chlorophyll a concentrations (>20 mg m-3) were also observed in autumn 2008 in the Central region, which is about twice as high as the maximum values typically observed in autumn throughout their time series. These results were further confirmed by spatial analyses, which showed that bloom conditions persisted throughout September and October 2008 in the Central region.
  • Results from the environmental drivers show positive SST anomalies predominated between 2003-2006 and 2013-2016 with the highest anomalies occurring in spring 2015. Strong positive anomalies in Fraser River discharge, coupled with strong negative wind anomalies, occurred in spring 2005 and 2015. CTD data were also used to calculate a stratification parameter, defined as the difference in density between the surface (average for the top 10 m) and 50 m. A higher stratification parameter is indicative of a more stratified water column. Results show that stratification was highest in Spring 2015 compared to the other years.
  • Statistical analyses indicate that chlorophyll a in the Northern SS is most highly correlated with SST and PAR, whereas chlorophyll a in the Central SS is most highly correlated with Fraser River discharge. Similar analyses carried out on the anomaly data revealed that chlorophyll a anomalies in both the Northern and Central SS were highly correlated with SST and PAR anomalies.