Dolly Varden (Salvelinus malma) is a char native to western North America that is harvested by northern communities for subsistence purposes. Populations found across northern Canada have experienced significant declines. Exploitation and local habitat change are the two main factors thought to have influenced these declines. Data to track trends in habitat quality, quantity, and use by Dolly Varden are lacking in the western Arctic. Thus there is a need for a research to achieve these challenges. This study details the development of a two-dimensional River2D (www.river2d.ca) hydrodynamic and habitat model to predict hydrodynamics and habitat availability for Dolly Varden for various flow scenarios. Intensive data in terms of bed bathymetry, water depth, velocity, substrate, and cover were surveyed for two spawning and overwintering reaches from Fish Hole Creek, a tributary to the Babbage River, and Little Fish Creek, a tributary to the Big Fish River, Canada. The model was calibrated by adjusting the bed channel roughness until good agreement of simulated versus surveyed water surface elevations at the open-water surveyed discharges were achieved. Predicted water surface, velocity, and habitat availability corresponded well with field measurements. Moreover, strong correlations and significant relationships were observed between the predicted and corresponding field values. The validity of the above calibrated River2D model was also confirmed through modeling other hydraulic and/or habitat parameters of interest. The developed River2D hydrodynamic and habitat model should be thus valid for hydrodynamic and/or habitat assessment for Dolly Varden fish species for various flows of interest.