Many uncertainties exist regarding riverine habitat use by fish during winter given the inherent challenges of sampling fish in periods of ice cover. Conventional sampling methods used during ice cover, such as traps and gill nets, are typically inefficient and exhibit species- and size-selective biases. While telemetry studies have proven useful, knowledge of over-wintering habitat use for juvenile fish or small-bodied species remains difficult to acquire under ice. Imaging sonar provides an innovative, unbiased means to assess habitat use of all fish during winter periods. This paper describes application of imaging sonar methods to investigate fish habitat use under ice in two contrasting environments: main channel habitats in the Athabasca River (a large boreal system in northern Alberta, Canada) and off-channel slough and tributary habitats in the Susitna River (a temperate system in southern Alaska, USA). Catch-per-unit-effort, occupancy, and relative abundance analyses were used to assess fish habitat relationships among habitat types, habitat characteristics, and time periods. Results validate imaging sonar as an effective tool to determine patterns of habitat use and evaluate effects of physical parameters (e.g., velocity and depth) on habitat use during periods of ice cover. Lessons learned, and limitations of imaging sonar methods are discussed.