Northeastern British Columbia (BC) is undergoing steady development for oil and gas extraction, mainly due to subsurface hydraulic fracturing (fracking), which requires significant quantities of water. Thus, it is of vital importance to obtain accurate long-term water balance information in the complex wetlands of northeastern BC to assist regulators to balance multiple priorities in a way that will not compromise the long-term sustainability of water resources, while minimizing ecological impacts. At the initial phase of this study, all fluxes of the Coles Lake water balance were measured for the 2013_2014 hydrological year. The total storage change was negative (-8.3 mm), and 2013_2014 was considered a relatively dry year. This study also quantifies the water balance fluxes within two boreal watersheds, the Coles Lake and Tsea Lake watersheds, through a combination of observational data analysis and numerical modelling using the MIKE SHE hydrological model for 1979_2014. MIKE SHE model calibration was performed manually based on snowmelt, pressure head, and streamflow, using a trial-and-error parameter adjustment procedure. Similar trends were observed for the Coles Lake and Tsea Lake watersheds although average of actual evapotranspiration (AET = 472.9 mm year-1) was higher while overland flow (OL = 26.3 mm year-1) was lower at the Coles Lake watershed compared to the Tsea Lake watershed (AET= 405.5 mm year-1 and OL = 48.5 mm year-1). Sensitivity simulations with the MIKE SHE model whereby the leaf area index was modified uniformly across the Coles Lake watershed to represent fully open, mixed and closed canopies provided further insights on the role of vegetation on the water balance. Simulated AET = 515, 529, and 558 mm year-1 and OL = 59, 46, and 11 mm year-1 for open, mixed, and closed canopies, respectively. Further, the Coles Lake forcing data were applied for the Tsea Lake watershed as a sensitivity test while other parameters remained unchanged. The variability of the vegetation canopies, and land cover including wetland distribution were the main contributors for different hydrological responses in these two watersheds. Baseline information generated by this study will support the assessment of the sustainability of current strategies for freshwater extraction.