Aquatic Habitat and Species

Toronto and Region Conservation Authority (TRCA) monitors fish communities, aquatic insects, habitat features, and temperatures within local streams as well as in Lake Ontario. TRCA offers a number of technical training workshops related to these topics.

What Do We Monitor and Why?

TRCA monitors the following key indicators to assess the aquatic health of our regional watersheds and the Toronto regional waterfront area in Lake Ontario:


Benthic macroinvertebrates are small organisms that live on the bottom of streams, rivers, and lakes. They can include insects, worms, mollusks and crustaceans. They are useful as water quality indicators because they have relatively long lifespans and are sensitive to changes in the aquatic environment. 

TRCA collects benthic macroinvertebrates annually at over 150 monitoring stations across the Toronto region. Over 45,000 benthic macroinvertebrates were collected in 2020 in support of the Regional Watershed Monitoring Program, habitat restoration projects, environmental assessments, and research studies. These data are used to monitor the health of aquatic ecosystems in the TRCA’s watersheds, assess the impacts of development projects, evaluate the effects of habitat restoration, and guide conservation decision-making. 

Members of TRCA’s aquatic monitoring team are provincial leaders in identifying benthic macroinvertebrates, with staff certified in genus level identification by the Society for Freshwater Science. 

Annually our team offersexternal training in Ontario Benthos Biomonitoring Network (OBBN) standardized sampling protocols to environmental professionals. OBBN is a multi-sector biomonitoring collaboration led by the Ontario Ministry of the Environment, Conservation and Parks, whereby members can share their data through a centralized database. 


Beginning in 2001, fish communities and their aquatic habitats have been surveyed in TRCA’s nine watersheds on three-year cycleas part of the Regional Watershed Monitoring Program (RWMP).  

2020 marked the sixth year where RWMP fish and habitat monitoring activities occurred within the Don River, Highland Creek, Mimico Creek, Petticoat Creek and Frenchman’s Bay watersheds. Monitoring follows the Ontario Stream Assessment Protocol (OSAP) and uses back-pack electrofishing methodology. Each fish is measured for length, weighed, identified to species, and released back into its environment. Over 5,000 individual fish records were collected in 2020. The aquatic habitat conditions are also assessed, including depth, width, stream temperature, and sediment type.

For Lake Ontario, nearshore fisheries surveys have been conducted in the Toronto Harbour since 1989. Fisheries surveys are used to track the effectiveness of restoration projects and Remedial Action Plan (RAP) measures for the Toronto & Region Area of Concern (AOC). Over 1 million individual fish records from close to 500 sites have been collected over the last three decades.

Additional stream and lake fish and habitat assessments, as well as fish rescues, are carried out within the Toronto region in support of various habitat restoration projects, environmental assessments, and research studies. 

TRCA also coordinates Aquatic Habitat Toronto (AHT), a group of agencies (municipal, provincial, federal) that have a common interest in improving the aquatic habitat along the Toronto WaterfrontAHT is focused on fulfilling the goals of the Toronto Waterfront Aquatic Habitat Restoration Strategy(TWAHRS). 

Learn more about the effectiveness of fish habitatrestorationusing TWAHRS techniques: 

Evaluating the effectiveness of aquatic habitat restoration implemented using the Toronto Aquatic Habitat Restoration Strategy


TRCA collects water temperature data using seasonal and year-round temperature loggers.

Temperature is a major factor that determines which aquatic species, fish, or bugs live in a particular stream. For example, Brook Trout rely on groundwater upwellings for spawning.

Tracking water temperature can also indicate the influence of groundwater on a watercourse. Toronto watersheds are historically dominated by coldwater stream conditions. The more urbanized the surrounding landscape becomes, the higher the water temperatures. This data helps to measure the effects of urbanization and climate change on stream health.

TRCA aquatic monitoring


Mosquito larvae populations are surveyed through the West Nile Virus Surveillance and Monitoring Program. The data collected are used to identify sites of potential concern or hotspots and then follow up with appropriate management actions. LEARN MORE.

TRCA West Nile Virus monitoring

What are the Data Telling Us?

This fisheries and aquatic habitat data report on the health and condition of the aquatic ecosystem and how its responding to changes in land use and climate. Several decades of scientific data on aquatic habitat and fish communities help inform: 

  • watershed-based planning,  
  • decisions around land-use changes,  
  • restoration opportunities,  
  • various development permit requirements, and  
  • legislation or policy change initiatives.  

Current Conditions: Streams 

The data is shared with our regional municipalities, various consultants, research institutions, and other organizations at the federal and provincial levels.  

Based on current data, the health of fish communities in streams are considered in ‘fair condition’ in seven watersheds and in ‘poor condition’ in three watersheds. This is determined using the Index of Biotic Integrity (IBI). 

Current Conditions: Waterfront 

The percent piscivore biomass (PPB) is used assess fish community health in the Lake Ontario nearshore. Using data from 2014-2018, there is an average biomass of 25% of resident piscivores (fish-eating fish) in sheltered embayments. This meets the target by RAP for the Toronto & Region Area of Concern (AOC).  

The continued aquatic habitat restoration efforts by TRCA and its partners, including those in support of the Don Mouth Naturalization and Port Lands Flood Protection Project, will continue to improve habitat conditions for fish communities. 


Rick Portiss
Senior Manager, Aquatic Monitoring and Management
Watershed Planning and Ecosystem Science