Canuels early research examined particles in the eastern tropical North Pacific Ocean, and lipid biomarkers in particles from North Carolina and San Francisco. She has examined the degradation of organic matter newly-placed on sediments, and anoxia in the Chesapeake Bay. Her research in Chesapeake Bay also considers how the source of organic matter to the bay impacts water quality. Canuels use of stable isotopes extends to examining stable isotope ratios in plants from San Francisco Bay, the use of stable isotopes to track sources of organic matter in estuaries,
how climate change will impact carbon cycling at the border between the land and the ocean and examining the age of organic matter in estuaries.