To advance our understanding of permafrost hillslope drainage dynamics and its influence on streamflow hydrochemistry, we instrumented a hillslope-stream sequence located in the headwaters of the Niaqunguk River watershed, Nunavut, Canada (63°N, 68°W). We combined high spatial resolution field measurements of water and frost tables across the hillslope, with semiweekly measurements of groundwater and streamflow chemistry to track the evolution of streamflow chemistry during active layer thaw. Interestingly, localized differential thaw patterns emerged under near saturation conditions across the instrumented hillslope, the result of a low-frequency high-magnitude summer rainfall event. Hillslope structure and uneven active layer thaw created two distinct fill-and-spill domains. A subsurface domain defined by frost table microtopography and a surface domain defined by surface topography. We observed a seasonal shift in streamflow chemistry with an increased influence of water flowing through the underlying mineral soils as the active layer thawed. As thaw progressed streamflow chemistry began to match that of the riparian groundwater, which was a mixture of hillslope surface and subsurface water. Hillslope-stream surface connections were sporadic and occurred when rainfall and saturation conditions across the lower portion of the hillslope were sufficient for water to spill out of midslope surface depressions and across a saturated riparian zone and into the stream. This research shows how hillslope structure and thaw processes influence hillslope-stream connectivity in permafrost terrain.