Hydrometric, isotopic and hydrochemical data were used to investigate runoff generation in a discontinuous permafrost headwater catchment. Research was undertaken between 10 April and 8 July 2008 within Granger Basin, a 7.6 km2 sub-catchment of the Wolf Creek Research Basin, Yukon Territory, Canada. The objectives of this research were to utilize hydrometric, stable isotope and hydrochemical methods to: (i) establish water balance components and (ii) couple water balance information with stable isotope and hydrochemical information to provide an enhanced understanding of runoff sources and pathways. The water balance components were snowmelt (152 mm), precipitation (68 mm), evaporation (88 mm), discharge (173 mm) and change in storage (−41 mm). The runoff ratio was high compared with previous years in this catchment. Using two-component hydrograph separation, pre-event water represented ∼73% of total discharge during freshet. End-member mixing diagrams suggested three contributing sources to streamflow in the following order: groundwater, soil water and snowmelt water. Concentration versus discharge diagrams identified the dilution of weathering ions during melt, while the ratio of potassium to calcium in streamwater suggests early contributions of pre-event water to discharge. Results from this research support previous work that pre-event water dominates freshet, yet the role of deeper groundwater is highlighted as an important contribution.