Temporal variations in ice sheet flow directly impact the internal structure within ice sheets through englacial deformation. Large-scale changes in the vertical stratigraphy within ice sheets have been previously conducted on centennial to millennial timescales; however, intra-annual changes in the morphology of internal layers have yet to be explored. Over a period of two years, we use autonomous phase-sensitive radio-echo sounding (ApRES) to track the daily displacement of internal layers on Store Glacier, West Greenland to millimeter accuracy. At a site located ~30 km from the calving terminus, where the ice is ~600m thick and flows at ~700m/yr, we measure distinct seasonal variations in vertical velocities and vertical strain rates over a two-year period. Prior to the melt season (March–June), we observe increasingly non-linear englacial deformation with negative vertical strain rates (i.e. strain thinning) in the upper half of the ice column of ~0.03 a-1, whereas the ice below thickens under vertical strain reaching up to 0.16 a-1. Early in the melt season (June–July), vertical thinning gradually ceases as the glacier increasingly thickens. During late summer to midwinter (August–February), vertical thickening occurs linearly throughout the entire ice column, with strain rates averaging 0.016 a-1. We show that these complex variations are unrelated to topographic setting and localized basal slip, and hypothesize that this seasonality is driven by far-field perturbations in the glacier’s force balance, in this case generated by variations in basal hydrology near the glacier’s terminus and propagated tens of kilometers upstream through longitudinal coupling.