The recent increase in fresh-water discharge during low-flow conditions as observed in many (sub-)Arctic Rivers has been attributed to a reactivation of groundwater flow systems caused by permafrost degradation. Hydrogeological simulations show how groundwater flow conditions in an idealized aquifer system evolve on timescales of decades to centuries in response to climate warming scenarios as progressive lowering of the permafrost table establishes a growing shallow groundwater flow system. Ultimately, disappearance of residual permafrost at depth causes a sudden establishment of deep groundwater flow paths. The projected shifts in groundwater flow conditions drive characteristic non-linear trends in the evolution of increasing groundwater discharge to streams. Although the subsurface distribution of ice will markedly influence the system response, current modeling results suggest that late-stage accelerations in base flow increase of streams and rivers, are to be expected, even if surface air temperatures stabilize at the current levels in the near future.