Estuary Monitoring Project

A guide to ongoing research and monitoring in the Annapolis River Estuary


The Annapolis Estuary

An estuary is the area where freshwater and saltwater intermix to create moderately saline, or 'brackish' waters. They are highly productive ecosystems that combine the physical and chemical properties required by marine, brackish, and freshwater organisms. The balance between freshwater and saltwater, the degree of tidal influence, and seasonal or physical factors such as wind and rainfall can all alter the chemical composition of an estuary ecosystem.

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The Annapolis Estuary

Estuaries that experience high tidal exchange and turbulent motion will efficiently mix the freshwater and saltwater inputs, creating similar conditions throughout the water column, known as a mixed estuary. In contrast, estuaries that experience high volumes of freshwater input but low tidal exchange will produce a water column that is distinctly separated into a surface freshwater layer, and an underlying salt water layer. This is referred to as a stratified or salt wedge estuary.

In the Annapolis system, the estuary receives freshwater input from a drainage area of over 1600 square kilometers, and saltwater input from the Bay of Fundy. It is a dynamic tidal system that flows 120km from the Annapolis River headwaters between Aylesford and Berwick all the way downstream to Digby Neck.

Prior to the construction of the tidal dam and causeway between Annapolis Royal and Granville Ferry in 1960, tidal exchange was unrestricted. The causeway introduced a barrier to tidal flow, and the resulting flow regime upstream has been greatly altered. What was previously a mixed estuary is now highly stratified, with a distinct separation between the surface freshwater layer and the underlying saltwater layer. This stratification persists at least 30km upstream of the causeway around Bridgetown, and the boundary between fresh and saltwater layers often falls between 1.5-2m below the water surface, though both of these measures fluctuate according to seasonal changes in rainfall, wind, and freshwater input.

Construction of the tidal dam and Annapolis Royal causeway, circa 1960

Stratified estuaries often have lower turbidity (a measure of cloudiness due to suspended particles), lower dissolved oxygen levels, and higher primary production compared to mixed estuaries. This demonstrates the potential for significant habitat alteration as a result of changing hydrology. In addition, the operation of the Annapolis Tidal Generating Station in 1984 introduced the threat of turbine-strike mortalities for migrating fish populations, and population declines were in fact observed in the following decades.

The species of greatest interest are Striped Bass, Atlantic Salmon, and Atlantic Sturgeon: the only three species predicted to experience high or extreme population-level impacts from turbine mortality in the Annapolis system. All three of these species demonstrate a high degree of uncertainty with respect to their current population size, population structure, and life history in the area. Addressing this gap in knowledge is thus imperative for the conservation and preservation of these species in the Annapolis River.


Timeline

PRE 1960

The Annapolis estuary is a mixed system with unrestricted tidal exchange

1960

Construction of the tidal dam and causeway imposes a physical barrier to tidal exchange upstream

1979

Studies identify altered hydrology and declining fish populations in the Annapolis River (Gibson et al. 2019)

1984

Annapolis Tidal Generating Station (ATGS) begins operation

1985

Continued decline of fish populations and increase in turbine-strike mortalities (Dadswell 2018)

1994

Last recorded evidence of Striped Bass spawning in the Annapolis River (Jessop 1995)

2006

Annapolis River Striped Bass population is deemed extirpated by DFO

2010

Southern Upland Atlantic Salmon population is classified as endangered by COSEWIC

2011

Maritimes population of Atlantic Sturgeon is classified as threatened by COSEWIC

2012

Bay of Fundy Striped Bass population is classified as endangered by COSEWIC

2019

ATGS ceases operation following system failure and a notice from DFO to seek an authorization under the Fisheries Act.

2021

The Clean Annapolis River Project establishes the estuary monitoring program

Species of Interest

The preliminary goal of the estuary monitoring program is to determine whether local populations of Striped Bass, Atlantic Salmon, and Atlantic Sturgeon persist in the Annapolis River, and to gather baseline data on how they utilize the habitat.

Striped Bass

Striped Bass (Morone saxatilis) are large-bodied fish belonging to the temperate bass family. They have a dark olive green back, white belly, and sides that fade to silver. Adults are characterized by the seven to eight dark horizontal stripes along their sides. Reaching up to 180cm in length, they are high-trophic predators in estuary and coastal ecosystems, preying on various invertebrates and small fish species. 

Adult Striped Bass

Striped Bass are anadromous fish, meaning that they inhabit both freshwater and saltwater environments at different points in their lifecycle. Often, spawning, incubation, and early larval stages occur in fresh or brackish water while juvenile and adult fish make use of coastal, estuarine and saltwater habitat. Winter is spent in the warmer waters of estuaries or freshwater habitats and in the spring, fish return to their natal river to spawn.

The Annapolis River once supported a healthy population of Striped Bass, but since the 1970s, population numbers have been in decline: a trend which is attributed to changes in water chemistry and circulation as a result of the causeway and the Atlantic Tidal Generating Station. In 2006, the Annapolis River Striped Bass population was classified as extirpated by Fisheries and Oceans Canada, owing to repeated spawning failures and negligible survival beyond the larval stage. It is thought that the Annapolis River may now serve only as foraging and over-wintering habitat, as spawning and nursery habitat features have been significantly degraded. 

Striped Bass caught in the Annapolis River, 1995

Since 2010, CARP has been working collaboratively with the  Striped Bass Research Team , based out of Acadia University, to support monitoring and research efforts in the Annapolis River watershed. The 2021 season marked the first time since 2015 that CARP conducted surveys targeting Striped Bass in the Annapolis River.

Canadian Striped Bass are divided into three populations:

1) St. Lawrence River population

2) Southern Gulf of St. Lawrence population

3) Bay of Fundy population

The Bay of Fundy population is further divided into three designatable units (DUs):

Terry Kelly

Saint John River, NB

Shubenacadie River, NS

Annapolis River, NS

The Shubenacadie River population is the only DU that is known to be reproductively active, and the Annapolis River population is thought to be extirpated.


Atlantic Salmon

Atlantic Salmon (Salmo salar) are a medium-sized salmonid with a pointed head and long streamlined body shape. Their coloration changes throughout their life cycle, depending on age and spawning status. They are anadromous fish, meaning they utilize both freshwater and saltwater habitats at different points in their life cycle. Spawning and early life stages take place in well-oxygenated freshwater streams. At the smolt stage, they migrate to the ocean to mature for 1-4 years before returning to their natal rivers to spawn.

Atlantic Salmon at different life and spawning stages

The Annapolis River Atlantic Salmon population falls under the Southern Upland population designatable unit (DU). Since 1996, salmon in this DU have declined by 61%, and as of 2000, the Department of Fisheries and Oceans predicted that 55% of rivers in this DU were extirpated, with an additional 36% at risk of extirpation. This population was listed as endangered by COSEWIC in 2010, citing altered hydrology, invasive fish species, and habitat fragmentation due to dams and culverts among the primary freshwater threats. Salmonid aquaculture and changes in marine ecosystems also pose a threat to marine survival, but the specific changes are not well understood.

Through CARP's fish habitat restoration project, salmon parr have been observed in the freshwater tributaries of the Annapolis River following habitat enhancement and restoration efforts. Click the link below to learn more about CARP's fish habitat restoration work.

The Maritime Region encompasses four designatable units (DUs) of Canadian Atlantic Salmon, all of which are endangered:

1) Eastern Cape Breton

2) Outer Bay of Fundy

3) Inner Bay of Fundy

4) Nova Scotia Southern Upland

The Annapolis River falls within the Nova Scotia Southern Upland designatable unit


Atlantic Sturgeon

Atlantic Sturgeon (Acipenser oxyrinchus oxyrinchus) are the largest anadromous species in the Northwest Atlantic. Females, the larger of the sexes, can reach up to 3 meters in length and 200 kilograms. They have distinctive bony projections along their body called scutes, and they can be distinguished from the only other sturgeon species found in Atlantic Canada, the Shortnose Sturgeon, by their longer snout and greater number of scutes. With an ancestry dating back over 200 million years, Atlantic Sturgeon are of great ecological importance.

The two species of sturgeon found in Atlantic Canada: Atlantic Sturgeon (top) and Shortnose Sturgeon (bottom)

Spawning occurs in rocky substrates of shallow freshwater, and young fish spend up to 6 years in fresh and brackish water before migrating to the ocean. Atlantic Sturgeon are a long-lived and late-maturing species, with a generation time of about 40 years; this makes them particularly susceptible to threats. Once matured, they may return to upstream sites in the fall or spring preceding spawning, and often overwinter in the deep estuarine channels downstream of spawning sites. Individuals may only spawn once every several years, making their presence even less predictable.

Adult Atlantic sturgeon

Very little is known about Atlantic Sturgeon in the Annapolis River, but juveniles and reproductive adults have both historically been reported in the system, and DFO suspects that a small spawning population may still persist. Anecdotal evidence from local anglers supports this claim. The Maritime population of Atlantic Sturgeon was listed by COSEWIC as threated in 2011, citing threats as habitat modification, barriers to migration, poor water quality, and a general lack of quantitative data. The long lifespan and late maturity of this species only increase the severity of these threats.

Atlantic Sturgeon in Canada are divided into the St. Lawrence DU and the Maritimes DU.

The Annapolis River falls within the Maritimes DU, which encompasses New Brunswick, Nova Scotia and the adjacent waters of the Atlantic Ocean.

There is a known breeding population of Atlantic Sturgeon in the Saint John River, and populations are thought to exist in other rivers around the Bay of Fundy.

Turbine strike mortalities as a result of the ATGS, as well as reports from local anglers and community members suggest that a small breeding population may still persist in the Annapolis River.


Objective

The main objective of CARP's estuary monitoring and research project is to fill knowledge gaps that will support the long-term restoration and stewardship of the Annapolis River estuary ecosystem, including the species-at-risk and other biodiversity it supports. Key knowledge gaps that we are currently focused on include:

1.

WHAT IS THE CURRENT SIZE AND STATUS OF LOCAL POPULATIONS OF STRIPED BASS, ATLANTIC STURGEON AND ATLANTIC SALMON?

2.

WHAT ARE THE MOVEMENT AND HABITAT USE PATTERNS BY THESE SPECIES IN THE ANNAPOLIS RIVER?

3.

WHAT ARE THE THREATS FACING THESE POPULATIONS?

VARIOUS METHODS ARE BEING USED TO ADDRESS THESE QUESTIONS, AND FILL THESE DATA GAPS.

These methods include fish sampling, acoustic monitoring, and water quality monitoring.

1.

WHAT IS THE CURRENT SIZE AND STATUS OF LOCAL POPULATIONS?

FISH SAMPLING

Fish Sampling

Conducting egg tow surveys on the Annapolis River, 2021

Employing sampling methods that target different life stages can provide a comprehensive overview of species presence in the estuary, and may help to identify the size and composition of local populations. Surveying for all life stages offers a way to identify the developmental stage which is most strongly contributing to population declines.

The sampling methods we are using include:

  • Egg tows ..................................... egg and larval stage
  • Beach seines ......................................... juvenile stage
  • Fyke netting ........................ juvenile and adult stage
  • Rod and reel angling ............................... adult stage

To date, egg tows, beach seines and fyke netting has been conducted to target Striped Bass. These efforts have focused on known historical spawning locations near the upper limit of the salt wedge, and at mudflat, sand, and cobble beaches along the Annapolis River and its tributaries.

Some of the species observed during beach seine surveys in 2021


Beach seines were conducted at 17 sites along the Annapolis River, Allain's Creek and Bear River. Each site was visited twice between July and November, and data on fish species, abundance, and size were recorded. Explore the map below to see what was found.

Jubilee Park

Jubilee Park. Click to expand.

Upper Granville

Upper Granville. Click to expand.

Tupperville

Tupperville. Click to expand.

Belleisle

Belleisle. Click to expand.

Roundhill Road

Roundhill Road. Click to expand.

Marsh Road

Marsh Road. Click to expand.

Head Pond

Head Pond. Click to expand.

Annapolis Royal

Annapolis Royal. Click to expand.

Allain's Creek

Allain's Creek. Click to expand.

Upper Clements

Upper Clements. Click to expand.

Cornwallis

Cornwallis. Click to expand.

Bear River

Bear River. Click to expand.

Smith's Cove

Smith's Cove. Click to expand.

Bear River Bridge

Bear River Bridge. Click to expand.

Raymond's Point

Raymond's Point. Click to expand.

Kniffen Hollow

Kniffen Hollow. Click to expand.

River Road

River Road. Click to expand.

Jubilee Park

Upper Granville

Tupperville

Belleisle

Roundhill Road

Marsh Road

Head Pond

Annapolis Royal

Allain's Creek

Upper Clements

Cornwallis

Bear River

Smith's Cove

Bear River Bridge

Raymond's Point

Kniffen Hollow

River Road

There has been no evidence of eggs, larvae, or juvenile Striped Bass, but over 20 catch records of adult striped bass were submitted through CARP's Volunteer Angler Program, including 14 scale samples for genetic analysis. These results indicate that adult Striped Bass still persist in the river, and the genetic analyses will determine whether these individuals constitute a local population, or are simply migrants from other populations.

Visit the  Volunteer Opportunities  page on the Clean Annapolis River Project website, or email carp@annapolisriver.ca to learn more about the Volunteer Angler Program, and how you can participate. Volunteer application forms can be filled out directly on the website, or through this  downloadable form .


2.

WHAT ARE THE MOVEMENT AND HABITAT USE PATTERNS BY THESE SPECIES IN THE ANNAPOLIS RIVER?

ACOUSTIC MONITORING

Acoustic Monitoring

“For species and life stages large enough to carry acoustic tags, advances with this technology afford the opportunity to address many of the data gaps.”   - DFO 2019 Review 

Acoustic monitoring technology allows for the passive tracking and monitoring of fish. For populations such as the striped bass and Atlantic sturgeon whose use of the watershed remains largely unknown, acoustic technology may help uncover information regarding migration patterns, and the locations of key foraging and overwintering habitat.

A network of acoustic receivers will be established throughout the estuary that will help track the movement of anadromous species.

Species of interest will be tagged with acoustic transmitter tags. These tags send out signals at a specific frequency that is picked up by the receiver units.

Acoustic receiver setup

As tagged fish move throughout the river, the receiver stations will pick up their unique signals, and gather data on which individual fish was detected at that location.

At present, CARP has established two acoustic receiver stations, and registered the project with the  Ocean Tracking Network : a global network for aquatic animal tracking and acoustic data management. Plans are in place to deploy receiver stations at additional sites during the 2022 season. Proposed receiver stations will target known spawning locations, and other areas thought to provide suitable foraging, nursery, or overwintering habitat. Receiver stations will also cover key pinch points along the river in order to optimize fish detection along migration routes. No fish have yet been tagged with acoustic transmitters, but these activities are scheduled to occur during the spring and summer of 2022.

Prospective acoustic receiver stations


3.

WHAT ARE THE THREATS FACING THESE POPULATIONS?

WATER QUALITY MONITORING

Water Quality

Water quality monitoring is one way to address questions about habitat suitability and threat to species of interest. Suitable water quality conditions are imperative for developmental success and survival of aquatic species. There exist optimal ranges of pH, temperature, salinity, and dissolved oxygen levels in which aquatic species can survive. Beyond these thresholds, survival can decline.

Quantifying the current water quality conditions in the Annapolis Estuary can provide insight into whether suitable habitat conditions for various life stages are present in the system. Water quality conditions that are not optimal could be driving population declines or spawning failures. Other factors that could influence survival include habitat structure such as substrate and flow rate, as well as community-level factors like predation or competition with other species.

Annapolis River, pre-causeway

Water quality sampling locations (blue are active sampling locations, and orange are stationary data logger locations)

The ecological differences between mixed and stratified estuaries are well documented, which means that changing hydrology can have severe effects. The management of water at the Annapolis Royal Tidal Generating station and causeway has the potential to significantly impact the ecology of the Annapolis estuary. Species that were adapted to a mixed estuary system may have had to alter their habitat use accordingly, or seek new habitat altogether when new management practices introduced new conditions. To gather water quality data in the Annapolis Estuary, a combination of passive data collection and active sampling is being conducted. Passive data are collected using small data loggers that collect temperature, light, and pressure information at regular time intervals. Active sampling is conducted using a handheld water quality probe that measures temperature, pH, salinity, and dissolved oxygen levels, among other parameters.

The results from sampling efforts in 2021 show notable differences between early and late season sampling with respect to salinity gradients, surface water temperatures, and dissolved oxygen saturation. The salt wedge appears to extend further upstream at the end of the season, and similarly, the levels of dissolved oxygen appear lower in the late season. These differences highlight the importance of continued monitoring; conducting surveys at different points in the seasonal and tidal cycles will produce a more comprehensive profile of the salt wedge in the Annapolis estuary. This will, in turn, aid in understanding how the salt wedge changes relative to the seasonal movements and habitat use by anadromous species. The profile of the thermal and saline stratification as observed on November 12th, 2021, between Bridgetown and Annapolis Royal can be seen below:

Halocline (salinity) and thermocline (temperature) profiles in November, 2021. Note that AR49 is located in Bridgetown and sites to the right are further west, ending in the Annapolis Basin at site AR83.

In addition, CARP has conducted water quality sampling in the Annapolis River since 1992 as part of the River Guardians water quality monitoring program. This program began as a community-based volunteer program, but since 2015, all monitoring work has been conducted by CARP staff. These results present a long-term dataset on the health of the Annapolis River between Aylesford and Bridgetown. Learn more about the River Guardians program by visiting the link below, and checking out the  2022 Annapolis Watershed Report Card .

In 2015, CARP partnered with Eastern Charlotte Waterways on a project that was part of the Gulf of Maine Council on the Environment's Ecosystem Indicator Partnership. This project focused on collecting water samples in estuaries to assess eutrophication indicators including nitrogen, phosphorous, and chlorophyll a. Water samples were collected from 20 monitoring sites in each estuary and sent to the lab for analysis. Results can be found on the Eastern Charlotte Waterways website.


Additional Activities

In collaboration with our partners at the Applied Geomatics Research Group at NSCC, we are also working to create flow and tide modelling scenarios to illustrate the flood risks and water level impacts resulting from various proposed management strategies for the Atlantic Tidal Generating Station in Annapolis Royal. The researchers at AGRG have collected bathymetric (depth) data using SONAR and LiDAR equipment in order to create a bathymetric map of the river both upstream and downstream of the existing ATGS. The following visual illustrates the regular tidal cycle upstream of Annapolis Royal for the hypothetical management scenario in which the causeway is completely removed. A full report, and additional visual aids will be made available on the Clean Annapolis River Project website.

Water levels during a typical tidal cycle in the open waterway scenario, NSCC AGRG 2022


Why is this work important?

Striped Bass, Atlantic Salmon and Atlantic Sturgeon are culturally, economically, and ecologically significant species, and so their conservation is of great importance. If we can gain a better understanding of how these species use the Annapolis Estuary, and identify their key habitat areas, we can focus restoration and enhancement efforts on these areas, and use this knowledge to inform management decisions that will minimize threats in the future.

Thank you to our project partners:

Acadia University

Applied Geomatics Research Group

Angler's Atlas

Atlantic Salmon Federation

Nova Scotia Community College

Nova Scotia Salmon Association

Striped Bass Research Team

and to our 2021-2022 funders:

Fisheries and Oceans Canada

Royal Bank of Canada

Clean Annapolis River Project, 2022

314 St. George Street, Annapolis Royal, NS B0S 1A0 (902)-532-753 carp@annapolisriver.ca

REFERENCES

DFO

 CSAS Science Advisory Reports 

COSEWIC

 Assessment and Status Reports 

Dadswell et al. 2018

 Long-term effect of a tidal hydroelectric propeller turbine on the populations of three anadromous fish species. Journal of Fish Biology. 

Gibson et al. 2019

 Fish mortality and its population-level impacts at the Annapolis Tidal Hydroelectric Generating Station, Annapolis Royal, Nova Scotia: a review of existing scientific literature. Canadian Technical Report of Fisheries and Aquatic Sciences. 

Jessop 1995

  Update on striped bass status in Scotia-Fundy region and proposals for stock management. DFO Atlantic Fisheries Research Document. 

Adult Striped Bass

Striped Bass caught in the Annapolis River, 1995

Adult Atlantic sturgeon

Conducting egg tow surveys on the Annapolis River, 2021

Annapolis River, pre-causeway

Saint John River, NB

Shubenacadie River, NS

Annapolis River, NS

Acoustic receiver setup

Acadia University

Applied Geomatics Research Group

Angler's Atlas

Atlantic Salmon Federation

Nova Scotia Community College

Nova Scotia Salmon Association

Striped Bass Research Team

Fisheries and Oceans Canada

Royal Bank of Canada