This study diagnoses the impact of projected changes in climate and glacier cover on the hydrology of several natural flowing Bow River headwater basins in the Canadian Rockies: the Bow River at Lake Louise (∼420.7 km2), the Pipestone River near Lake Louise (∼304.2 km2), the Bow River at Banff (∼2192.2 km2) all of which drain the high elevation, snowy, partially glaciated Central Range, and the Elbow River at Calgary (∼1191.9 km2), which drains the drier Front Ranges and foothills, using models created using the modular, flexible, physically based Cold Regions Hydrological Modelling platform (CRHM). Hydrological models were constructed and parameterised in CRHM from local research results to include relevant streamflow generation processes for Canadian Rockies headwater basins, such as blowing snow, avalanching, snow interception and sublimation, energy budget snow and glacier melt, infiltration to frozen and unfrozen soils, hillslope sub-surface water redistribution, wetlands, lakes, evapotranspiration, groundwater flow, surface runoff and open channel flow. Surface layer outputs from Weather Research and Forecasting (WRF) model simulations for the current climate and for the late 21st century climate under a “business-as-usual” scenario, Representative Concentration Pathway 8.5 (RCP8.5) at 4-km resolution, were used to force model simulations to examine the climate change impact. A projected glacier cover under a “business-as-usual” scenario (RCP8.5) was incorporated to assess the impact of concomitant glacier cover decline. Uncalibrated model simulations for the current climate and glacier coverage showed useful predictions of snow accumulation, snowmelt, and streamflow when compared to surface observations from 2000 to 2015. Under the RCP8.5 climate change scenario, the basins of the Bow River at Banff and Elbow River at Calgary will warm up by 4.7 and 4.5 °C respectively and receive 12% to 15% more precipitation annually, with both basins experiencing a greater proportion of precipitation as rainfall. Peak snow accumulation in Bow River Basin will slightly rise by 3 mm, whilst it will drop by 20 mm in Elbow River Basin, and annual snowmelt volume will increase by 43 mm in Bow River Basin but decrease by 55 mm in Elbow River Basin. Snowcovered periods will decline by 37 and 46 days in Bow and Elbow river basins respectively due to suppressed snow redistribution by wind and gravity and earlier melt. The shorter snowcovered period and warmer, wetter climate will increase evapotranspiration and glacier melt, if the glaciers were held constant, and decrease sublimation, lake levels, soil moisture and groundwater levels. The hydrological responses of the basins will differ despite similar climate changes because of differing biophysical characteristics, climates and hydrological processes generating runoff. Climate change with concomitant glacier decline is predicted to increase the peak discharge and mean annual water yield by 12.23 m3 s−1 (+11%) and 11% in the higher elevation basins of the Bow River but will decrease the mean annual peak discharge by 3.58 m3 s−1 (-9%) and increase the mean annual water yield by 18% in the lower elevation basin of the Elbow River. This shows complex and compensatory hydrological process responses to climate change with the reduced glacier contribution reducing the impact of higher precipitation in high elevation headwaters and drier soil conditions and lower spring snowpacks reducing peak discharges despite increased precipitation during spring runoff in the Front Range and foothills headwaters under a warmer climate.