The principal aim of Dr. Cunjak’s research program is the ecology of riverine fishes with special interest in the conservation of Atlantic salmon. There are four main areas of focus for his research: winter biology, anthropogenic impacts, critical fish habitats in rivers and energy flow in stream food webs. His research approach to winter biology involves studies of fish movement and habitat-use, energetic costs of overwintering, and the impact of river ice on egg survival and habitat availability.

A major research focus has been the quantification of forestry and agriculture impacts in stream ecosystems. These anthropogenic impacts have been considered in relation to hydrology, sediment loading, nutrient cycling, food webs and water temperature. In studying critical habitats in rivers, his research has quantified and considered the importance of refugia in river systems during in-stream stressor events (e.g. floods, ice break-up, high temperature) using Atlantic salmon as the indicator species for population-level responses.

Currently, Dr. Cunjak uses stable isotopes as a tool in distinguishing food source origins for riverine food webs, and for assessing the importance of marine-derived nutrients delivered by diadromous fishes in sustaining freshwater productivity in Atlantic rivers.