Fall science survey in the Scotian Shelf and Bay of Fundy

From September 28 to October 21, 2025, our scientists will be onboard the Royal Research Ship (RRS) James Cook for a multidisciplinary science survey.

We are collecting data, samples, and observations in support of:

• The Atlantic Zone Monitoring Program. This program collects baseline biological, chemical and physical oceanographic data, which has uses across the Department.
• Cetacean research and monitoring. Information on cetaceans, such as whales, dolphins and porpoises, helps inform our management decisions.
• The North Atlantic right whale foraging habitat assessment project. We are collecting samples of zooplankton to better understand where endangered North Atlantic right whales forage.

This survey supports scientific goals for our department and other federal departments, as well as external research and academic organizations.

Regular updates will be posted to this webpage, so you can follow along our science journey!

Follow our journey

• November 10: Our final survey stops

  After a brief time in port to conduct a crew change and for Mi’kmaw partners to join us onboard the RRS James Cook, we continued our collective mission across the Scotian Shelf to conclude the fall science survey. These final operations focused on knowledge sharing, while recovering an array of six passive acoustic monitoring moorings deployed in the Cabot Strait, and collecting comprehensive oceanographic data and samples from AZMP stations located in the Cabot Strait and within the St. Anns Bank Marine Protected Area (MPA).

  

  St. Anns Bank MPA is an area of shared importance between DFO and the Mi’kmaq of Nova Scotia, which we jointly manage to ensure Indigenous and Western knowledge are equally considered in the study and protection of this unique underwater area.

  The Cabot Strait is a busy waterway with significant vessel traffic presence, including shipping lanes and a major ferry route. This is also an important movement corridor for whales into and out of the Gulf of St. Lawrence, including North Atlantic right whales, who seasonally gather in the Gulf. Vessel strikes are a threat to North Atlantic right whales and other whale species, and passive acoustic data helps us understand when and where whales pass through this area, so we can make more informed decisions on how to best protect them.

  

  We concluded the survey in the St. Anns Bank MPA, where we collected data and samples to support ongoing monitoring efforts to better understand the physical, chemical, and biological oceanographic variability of this important region. While in the MPA, we also collected eDNA samples to evaluate the diversity of species and potential presence of invasive species within the area as part of a collaborative project with our Mi’kmaq partners across Nova Scotia.

  

• October 16: Returning to the Bedford Institute of Oceanography

  The RRS James Cook has returned to the Bedford Institute of Oceanography for a crew change as the first leg of the fall science survey comes to a close. Over the past several weeks, the team has:

  - sampled upwards of 70 hydrographic stations

  - retrieved and deployed passive acoustic moorings in six priority areas

  - collected over 100 zooplankton samples

  - observed 10 marine mammal species

  

  

  

  Collecting this critical ocean data helps us better understand ocean health, climate impacts, and food webs that support fish stocks and marine mammals—providing the long-term, consistent data needed to track changes in our Maritimes Region.

  In addition to the operations required to collect the ocean data, fundamental science work also takes place in the lab, where hundreds of samples are carefully processed each day. Scientists and technicians meticulously filter water samples to isolate and extract specific components, like chemicals, nutrients, and plankton for analysis. This time-consuming and precise process transforms raw field samples into meaningful scientific data, forming the backbone of the insights we gain about ocean health and change.

  

  Behind every water sample collected and every instrument deployed, the critical task of data management is working in the background. Just as vital as the science itself, this behind-the-scenes effort ensures that the information gathered is not only preserved, but remains accurate, consistent, and usable long after the survey ends. Through clear protocols, regular backups, careful equipment monitoring, and detailed documentation, reliable scientific records are created that will support research, policy, and decision-making for years to come.

  

  Another cornerstone of the survey’s success is something that underpins every action on board: safety. Whether navigating open waters or conducting scientific operations, safety is always the first priority. Every deployment, sample, and decision is the result of close coordination between scientists, technicians and crew, each relying on one another’s expertise. It’s a team effort grounded in trust, professionalism, and a shared commitment to doing the job right, and doing it safely.

  As the first leg of the fall survey wraps up, a number of milestones have been met thanks to the dedication of the entire survey team. Their work underpins critical science advice that supports sustainable fisheries, marine conservation, and safe navigation.

  In a time of rapid ocean change, reliable, long-term data is more important than ever. Together, through these bi-annual scientific surveys, we continue to advance our understanding of the North Atlantic Ocean, and in turn, better support Atlantic Canada’s marine industries, communities, and ecosystems, for generations to come.

  

• October 10: From the Halifax Line to Logan Canyon and the Gully

  Following operations in the Roseway Basin, the RRS James Cook headed to the AZMP’s ‘Halifax Line.’ That's a set of 11 hydrographic stations beginning southeast of Halifax, spanning across two conservation areas (Emerald Basin and Emerald Bank) to approximately 230 kilometers offshore. The Halifax Line is one of the AZMP’s longest-standing sources of observational data on the hydrographic structure of the Scotian Shelf, dating as far back as the 1880s, when it was first sampled as part of the Halifax-Bermuda section during a voyage of the H.M.S. Challenger. As of 1998, it became part of our AZMP, selected for its historical data set, proximity to the Nova Scotia Current (a dominant inflow originating in the Gulf of St. Lawrence), and capacity to sample both shelf and slope waters.

  Sampling of the Halifax Line while on board the RRS James Cook included the deployment of the CTD-Rosette and vertical ring net tows at all stations. Additional sampling included use of the MultiNet and Video Plankton Recorder near Emerald Basin. We also retrieved and deployed a long-standing oceanographic mooring designed to monitor changes in the Nova Scotia Current.

  The next operation took place approximately 40 kilometers south of Sable Island, in Logan Canyon, where a passive acoustic monitoring (PAM) mooring was deployed. This area has been identified in the Scotian Shelf-Bay of Fundy Conservation Network as a Tier 2 site for potential future protection. Data collected by PAM moorings allows our scientists to listen for whales and other underwater sounds – creating a more fulsome picture of the area’s biodiversity and acoustic environment.

  

  Next, the vessel traveled approximately 50 nautical miles along the edge of the Scotian Shelf to the Gully Marine Protected Area (MPA). The Gully is Atlantic Canada's largest submarine canyon and Canada’s oldest Oceans Act MPA. This important ocean habitat is home to the endangered Scotian Shelf population of Northern Bottlenose Whales, as well as many other species of whales and dolphins.

  

  Over the span of a day, the team conducted acoustic mooring retrievals and deployments, CTD-Rosette sampling, and vertical ring net tows. Marine mammal observers also sighted pilot whales, grey seals, common dolphins and northern bottlenose whales during our visit. These activities support a variety of departmental priorities including species at risk, MPA monitoring, marine conservation targets, and broader whale research initiatives.

  

  The Gully MPA Management Plan outlines the conservation-related goals for the area, which include protecting the MPA’s natural biodiversity, physical structure and physical and chemical properties, while maintaining productivity of the ecosystem. The data collected from the CTD-Rosette allows us to monitor changes in these factors, year after year.

  PAM moorings also play a key role in monitoring the Gully MPA. They are used to assess the presence of whales while also measuring underwater noise levels. Monitoring the Gully’s acoustic environment to understand if and how it may be changing over time is an important activity, as acoustic disturbance is a threat to Northern Bottlenose Whales and other whale species in the area.

  

  

• October 8: The RRS James Cook motors on

  At nearly every station, the CTD/Rosette dives into the water once again, but no two deployments are the same. Each one seeks answers to a different scientific question. In addition to collecting data and samples that help us understand changes in ocean health, we also use the CTD/Rosette to extract water samples so we can learn more about the species that are present in our waters. We accomplish this by analyzing environmental DNA (eDNA), genetic material shed by organisms into their environment.

  

  We use a vacuum pump water sampling system to filter water samples collected from the CTD/Rosette, separating the genetic material from the water so that it can be extracted for further analysis. The extracted DNA will later be duplicated using a process called Polymerase Chain Reaction (PCR) amplification, which produces many copies of the DNA of a targeted gene region. Because each species has a unique signature encoded within their DNA, these copies can be used to identify which species are present with a measurable level of confidence.

  

  As we travel through the Fundian Channel-Browns Bank Area of Interest (AOI), species mapping, invasive species detection, and biodiversity monitoring becomes crucial. Environmental DNA provides a non-invasive way to study biodiversity in these sensitive and species-rich ecosystems. By collecting and analyzing eDNA from the water, we can learn about the many species that inhabit this special area and use that knowledge to help guide conservation efforts. Ring net tows were also performed across the AOI, to further our understanding of North Atlantic right whale (NARW) feeding patterns in this area.

  After concluding operations in the Fundian Channel-Browns Bank AOI, we entered Roseway Basin, another critical habitat for the NARW, where this endangered species is known to feed and socialize. Here, we recovered and deployed an acoustic mooring, performed several ring net tows, and also used two new pieces of equipment, the Video Plankton Recorder (VPR) and a MultiNet system.

  The VPR is an underwater video microscope that provides high-resolution data on the composition of plankton. The VPR is deployed like a yo-yo, repeatedly raised and lowered to the seabed, creating vertical profiles of zooplankton distribution. This method of sampling does not damage the organisms being observed, allowing fragile plankton and particles to be quantified.

  

  The MultiNet, or Multi Plankton Sampler, contains five separate nets, each with their own collector to recover samples from different depth ranges. This specialized tool not only helps us learn which plankton species are present at each depth, but also which stage they are in their life cycle. All of the data collected from these various sampling methods support a more clear and fulsome understanding of NARW prey distribution across this critical habitat area, especially as ocean conditions change over time.

  

  While the marine mammal observers have not sighted any NARW’s, an acoustic detection was made only two days before our visit. Any NARW sightings and acoustic detections are logged in Whale Insight, Fisheries and Oceans Canada’s interactive whale tracker.

  

  Next, we will deploy an acoustic mooring in Logan Canyon, an area identified for potential future protection, before making our way to The Gully Marine Protected Area (MPA) – Canada’s oldest MPA!

  

  

• October 3: Let the scientific activities begin!

  We’re a few days into our multi-faceted fall science survey, which is taking place across the northwest Atlantic continental shelf.

  Our first scientific operations took place just outside Halifax Harbour, where our Conductivity, Temperature, Depth (CTD) Rosette was deployed to collect sensor data and water samples. Two vertical ring net tows were performed to capture samples of tiny zooplankton. The data and samples collected with these instruments inform the Atlantic Zone Monitoring Program (AZMP) objectives. 

  

  

  The data and samples from the CTD Rosette help us understand how the physical, chemical and biological state of the Atlantic Ocean changes over time, by comparing year over year data collected on these twice-yearly surveys. Each deployment helps us learn more about the health of a specific ocean area.

  Since the vessel’s departure, the CTD Rosette has collected over 500 unique samples across Atlantic Canadian waters and into the Gulf of Maine. These samples are used along with data from satellite remote sensing systems to describe changes in phytoplankton biomass and annual production cycles in AZMP state of the ocean reporting.

  One focus of the program is phytoplankton. Like trees and other green plants turn sunlight into energy, phytoplankton (microscopic, chlorophyl filled organisms) absorb light and perform photosynthesis in our waters. This essential process is responsible for at least 50 per cent of the Earth’s oxygen production, supporting marine life, as well as life on land – the air you breathe may just be thanks to these small, but mighty, marine organisms.

  

  Phytoplankton are also essential to the marine food web, providing nutrients for prey species like zooplankton – a common food source for a variety of fish and other marine creatures, including the endangered North Atlantic right whale (NARW). In fact, we use data from ring net tow samples to determine the abundance and distribution of zooplankton, which informs our understanding of where NARW feed.

  

  In turn, we use this information to support evidence-based management decisions aimed at protecting this endangered species. So far, we have collected over twenty zooplankton samples, from the outskirts of Halifax Harbour and into the Bay of Fundy, to the Gulf of Maine and back to a station at the edge of the Fundian-Channel Browns Bank Area of Interest.

  We also learn about NARW and other whale species through passive acoustic monitoring (in other words, by listening for whales), a main objective of the Cetacean Research and Monitoring Program (CRMP). On day two of the survey, the team retrieved and deployed acoustic moorings at their Grand Manan station in the Bay of Fundy. The Grand Manan Basin is identified critical habitat for the NARW. Our recording devices typically sit on the ocean bottom for up to a year, helping us learn about the presence of whales in our waters, through all seasons, even when we can’t see them.

  

  Another aspect of the CRMP’s work is collecting information about marine mammal observations. Each day, our marine mammal observers monitor the surrounding waters for any visible signs of cetaceans (whales, dolphins, and porpoises).

  

  As of day five of the survey, the observers and other on-lookers have spotted several pods of common dolphins, a sperm whale, humpback whales, a fin whale, as well as possible sei whale sightings.

  

  There’s more in store to learn and explore – check back soon for our next update!

   

• September 29: Departing from the Bedford Institute of Oceanography (BIO) 

  The RRS James Cook departed BIO in Dartmouth, Nova Scotia and travelled through the Halifax Harbour. Throughout this survey, we are visiting over many stations on the Scotian Shelf and in the Bay of Fundy.

  During the survey, we’ll collect a lot of data. We’re collecting biological data, chemical data, and physical data. Collecting this data consistently helps us create a baseline understanding of our marine environment. That’s important so we can better detect and understand changes in our ocean ecosystem.

  We’ll also retrieve and deploy scientific equipment along the way. One of the technologies we’re using is acoustic moorings, which detect and record whale calls. Acoustic data helps us better understand cetacean distribution, movement, habitat, and behaviour.

  We’re also using ring nets and a specialized Video Plankton Recorder to collect samples of tiny zooplankton. Then we’ll be able to generate fine-scale patterns of where zooplankton are. Zooplankton are a prey species for endangered North Atlantic right whale, so understanding where zooplankton are will help us understand where right whales feed.

  Among our science team are trained marine mammal observers. If marine mammals make an appearance on our survey, we’ll be ready to record information about the sighting, while staying a safe distance away.

  The survey is just getting started. Make sure to check back for another update on our science activities soon!

  

  Date published: September 29, 2025

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