Research and monitoring

Our research scientists, biologists and technicians lead and deliver an innovative and collaborative research program in aquatic ecology and hydrology.

The research focuses on:

  • Inland and Great Lakes:
    • lake ecosystems and how they function
    • ecology and life histories of native species
    • effects of manmade factors (such as fishing, invasive species and climate change)
  • Aquatic biodiversity and watersheds:
    • ecology and hydrology of rivers and streams
    • conservation genetics of native species
    • species at risk, their habitats and sampling methods
    • effects of manmade factors (such as climate change and development)

Through aquatic research, we:

  • research and provide expert advice about Ontario’s lake and river ecosystems and species to inform policy development and resource management decisions
  • develop:
    • aquatic monitoring survey designs, sampling methods, and analysis techniques
    • diagnostic tools and indicators to measure ecosystem and species health
    • models and decision-support tools to describe how systems function, predict future states, and define uncertainty
    • innovative uses of new technologies to sample ecosystems and species
  • collaborate in the delivery of aquatic research to meet ministry science priorities, with universities and other agencies

There are 4 key research areas (largest to smallest):

  • Great Lakes
  • rivers and streams
  • inland lakes
  • aquatic biodiversity

Great Lakes

Great Lakes and Lake Simcoe

Our research explores how invasive species and man-made activities affect ecosystems. We use a variety of cutting-edge tools, including:

  • hydroacoustics
  • simulation modelling
  • stable isotope analyses

Our research investigates:

  • the impact of invasive species on food webs
  • pelagic prey fish dynamics
  • simulation models for the sustainable harvesting of exploited fish populations
  • how to inform ecosystem management
  • hydroacoustics to study spatial ecology of fish and ecosystem changes
  • the effects of offshore wind power projects on fish and fish habitat and the science-based options for offshore wind power projects
  • the association between habitat and nearshore fish biodiversity
  • evolutionary ecology of fishes, including the management implications of fisheries-induced evolution


Food webs

We investigate the effects of ecosystem change (invasive species, climate change, habitat alteration) on the structure and function of aquatic food webs in the Great Lakes.

By combining field observation with controlled laboratory studies and simulation modelling, we try to identify vital rates (growth, production, transfer efficiencies) within and between different food web components. Through extensive collaboration with other agency and academic partners, we combine traditional methods with emerging technologies (sucha as ecological tracers and physiologic assays) to better resolve the food web composition and interactions.

Improving our understanding of these ecosystems and the impacts of various stressors reduces uncertainty in management. This leads to a more productive and sustainable use of resources.

Our research investigates:

  • ecological consequences of invasive Hemimysis anomala (bloody red shrimp)
  • factors influencing yellow perch recruitment
  • development of a control strategy for round goby
  • the influence of invasive species and climate change on lake whitefish
  • development of indicators of aquatic ecosystem health
  • bioenergetics and physiology of fishes


Population, decision support and climate change models

This research focuses on fish population dynamics, with a special emphasis on recruitment. We apply interdisciplinary knowledge to study fish recruitment. The results from fish population studies provide scientific advice on fish stock assessment and fisheries management.

This program area is also interested in modelling fish habitats. It studies how fish and their habitat respond to environmental changes like climate change.

Our research investigates:

  • the Lake Erie walleye population and management to inform sustainable harvest models
  • climate change modelling to predict the implications to fisheries management


Rivers and streams

River and stream aquatic ecology

Research and river and stream ecology focuses on the ecology and management of flowing waters. Understanding rivers requires a multidisciplinary ecosystem approach. Ecology, hydrology and geomorphology, are incorporated at various levels of temporal and spatial resolution (such as landscape ecology and GIS).

Students, collaborators, and the ministry staff are interested in the interaction of stream fishes and invertebrates at the population and community levels within their habitat. Laboratory and field experiments are combined with broad-scale comparisons of the structure and function of flowing waters.

Much of our research is applied in nature which serves to better the understanding and management of Ontario’s flowing waters. Basic science is needed in many cases to answer applied questions.

Our research investigates:

  • ecosystem effects of hydropower on rivers including spatial patterns of algae, organic matter, benthos and fishes, invertebrate drift response, the growth and migration of fishes and thermal regime characteristics
  • development of broad-scale monitoring programs for Ontario’s rivers including the development of sampling methods, an aquatic ecological classification systems, measures to describe the state of flowing waters (indicators) and a statistical reporting framework
  • regional and temporal variation of thermal and flow regime characteristics in Ontario’s rivers and their response to landscape and climatic change
  • species of concern including Atlantic salmon, redside dace, lake sturgeon, coaster brook trout


Hydrology and environmental flows

Our broad research interests include physical hydrology, GIS and remote sensing applications in hydrology, and linkages between hydrology and aquatic ecology. These interests cover a range of temporal and spatial scales, but we are particularly interested in basin-scale processes.

Our current research focuses on riverine processes and the impact of hydrologic alteration by dams and waterpower facilities on the ecological condition of river ecosystems.

Outcomes of the research will increase understanding of hydrological, biogeochemical and fluvial geomorphological processes and their relationship to the ecological integrity of river ecosystems.

Our research investigates:

  • geography of water – regional hydrology of Ontario
  • simulating natural flow regimes in ungauged basins to establish reference conditions for environmental flow assessments
  • characterizing natural and altered flow regimes using ecologically meaningful hydrologic indicators that can predict and explain changes in river condition
  • classification of natural and altered flow regimes
  • elucidating changes to physical riverine processes (i.e. hydrologic regime, sediment regime, water quality) in response to the alteration of river systems for waterpower
  • development and implementation of a framework and associated methodologies and tools to conduct environmental flow assessments


Inland lakes

Inland lake ecology and fisheries

Ontario has approximately 250,000 inland lakes that provide water, recreational opportunities and socioeconomic services to the people of Ontario. In 2008, the Ministry initiated the Broad-scale Monitoring for Inland Lakes program whereby hundreds of lakes are sampled using a standardized full ecosystem approach. This information allows us to learn more about the ecology of inland lakes, fisheries resources, and angler behaviour.

We also investigate:

  • indicators and reference points for assessing lake ecosystem and fisheries health
  • the effectiveness and design of inland lake monitoring protocols
  • community, spatial and metabolic theories of ecology
  • the utility of novel acoustic and imaging tools to monitor lake communities
  • traditional and novel quantitative approaches in fish production, community and ecosystem modelling
  • the effectiveness of conservation actions, and fisheries management and regulations
  • impacts of climate change and invasive species on lake communities and fisheries resources
  • cumulative effects of human activities on aquatic resources

Outcomes of our research improve our understanding of lake ecology, the methods that can be used to monitor lakes and fisheries, and the impacts of human activities on fisheries resources. We provide diagnostic and decision support tools that can inform conservation and management actions across the province.

Northern fish communities

The boreal shield is the largest ecoregion of Ontario and contains most of the province’s lakes. Fish communities of these lakes support important recreational and subsistence fisheries.

This program seeks to improve our management of these northern fisheries by refining our understanding of the ecological processes acting within and upon fish communities. The primary research themes are fish community structure and reproductive ecology.

Research is underway to:

  • examine variation in both the fish species composition and food web structure of northern lakes
  • learn how these influence energy and contaminant flow through systems
  • examine the influence of fish population demographics (age and size structure) and fisheries management practices on reproductive success

Our research investigates:

  • food web structure of northern lakes in relation to their physical characteristics and fish community composition
  • relative influence of food web position and growth rate on mercury bioaccumulation in northern piscivores
  • trophic niche overlap of co-habiting smallmouth bass and walleye with respect to water clarity
  • ecology of burbot in northern lakes
  • contrasting interpretations of fish community structure through NORDIC and broad-scale monitoring surveys
  • the relative roles of maternal and environmental effects on egg quality variation in northern fishes


Algonquin Provincial Park and beyond

Our program focus provides new knowledge about lakes inside and outside of Algonquin Provincial Park within the Algonquin land claim area.

Results from hydroacoustic and netting surveys are important for harvest and allocation questions as well as for park values, such as species conservation and representation of unique aquatic food webs. Also, to develop monitoring and assessment methods for understanding long-term population dynamics of sport fish such as lake trout, brook trout and smallmouth bass.

Our research investigates:

  • developing population assessment methods for fish and waterbird populations
  • ecology of brook trout, lake trout and other coldwater fish in Algonquin Park
  • conservation biology and species at risk research on Algonquin Park fish and fish assemblages, blackfin cisco and other species
  • recruitment dynamics of smallmouth bass and use of tournaments as fishery monitoring tools


Aquatic biodiversity

Aquatic biodiversity conservation

Our research program focuses on identifying and addressing information gaps relating to the biodiversity, conservation, and sustainable management of exploited and endangered aquatic species in Ontario to help ensure their long-term sustainability. This work is done through active collaborations with universities, other agencies and non-government organizations, as well as direct science support and collaboration with other research, management and field units within the ministry.

Much of our research uses genetic tools to assess the influences of environmental and manmade factors on the genetic structure and diversity within and among aquatic populations. Lab analyses are complemented by field experiments, assessment of field populations, and experimental rearing and life history trials at the ministry's Codringtion Fisheries Research Facility. Assessing genetic traits at the molecular and whole-organism levels enables us to weigh the comparative fitness of populations with differing adaptations, as well as determine the heritability of ecological and adaptive traits.

We are applying these combined tools to evaluate rehabilitation efforts for several species, as well as gauging the adaptive potential of coldwater species in response to climate change and novel stressors.

Our research investigates:

  • environmental DNA detection (eDNA) of aquatic invasive and endangered species
  • genetic stock structure of Great Lakes fishes
  • effects and effectiveness of stocking practices for inland fish populations
  • genetic biodiversity of exploited and endangered fish and mussel species
  • comparative fitness of wild, hatchery, and mixed-ancestry fish
  • genetic assessment of species rehabilitation and reintroduction efforts
  • effective population size and adaptive potential of coldwater species


Species at risk

This research program provides aquatic-based science support for implementing the provincial Endangered Species Act and federal Species at Risk Act.

Research contributes to species status assessments, addresses priority actions identified in government response statements and recovery strategies, and assists in defining habitat needs for species at risk. We have undertaken projects on a wide range of imperiled aquatic taxa, including freshwater mussels and fishes.

Our research investigates:

  • methods to monitor species at risk and describe their habitats
  • effectiveness of actions to protect and recover species at risk
  • impact of human activities (such as urbanization andflow regulation) on species at risk and their habitats
  • impacts of invasive species (such as round goby and phragmites) on species at risk
  • taxonomy, ecology and recovery of imperiled coregonids (deepwater ciscoes and lake whitefish species pairs)