Perennially flowing groundwater discharges along a 15-km section of the Fishing Branch River, Yukon causing open water during winter and numerous discrete springs near Bear Cave Mountain. Groundwater flow occurs in karstified marine carbonate rocks as well as in alluvial river talik(s). The PCO2 and δ13C indicate groundwater dissolves CO2 during recharge in organic soils and weathers limestone in the aquifer. These analyses show three groundwater chemistry groups and variability in surface water chemistry. The variations in water chemistry are related to differences in the rocks exposed in the recharge area. The δ18O and δ2H results show that groundwater represents approximately the annual average of precipitation based on samples collected in the region. Noble gases were used to determine that the recharge temperature lies between 0 and 5 °C which suggests that recharge happens during the summer. Groundwater ages, calculated using 3H-3He dating, were found to be between 0 and 17.7 years. River discharge was measured during spring and summer under different water-level conditions. Winter baseflow was calculated based on summer discharge measurements and the width of the river channel in winter. Although river flow decreases in winter, groundwater discharge maintains open water. Copyright © 2012 John Wiley & Sons, Ltd.