The warming trend in the Arctic region is expected to cause drastic changes including permafrost degradation and vegetation shifts. We investigated the spatial distribution of ice content and stable isotopic compositions of water in near-surface permafrost down to a depth of 1 m in the Indigirka River lowlands of northeastern Siberia to examine how the permafrost conditions control vegetation and microtopography in the Taiga-Tundra boundary ecosystem. The gravimetric water content (GWC) in the frozen soil layer was significantly higher at microtopographically high elevations with growing larch trees (i.e., tree mounds) than at low elevations with wetland vegetation (i.e., wet areas). The observed ground ice (ice-rich layer) with a high GWC in the tree mounds suggests that the relatively elevated microtopography of the land surface, which was formed by frost heave, strongly affects the survival of larch trees. The isotopic composition of the ground ice indicated that equilibrium isotopic fractionation occurred during ice segregation at the tree mounds, which implies that the ice formed with sufficient time for the migration of unfrozen soil water to the freezing front. In contrast, the isotopic data for the wet areas indicated that rapid freezing occurred under relatively non-equilibrium conditions, implying that there was insufficient time for ice segregation to occur. The freezing rate of the tree mounds was slower than that of the wet areas due to the difference of such as soil moisture and snow cover depends on vegetation and microtopography. These results indicate that future changes in snow cover, soil moisture, and organic layer, which control underground thermal conductivity, will have significant impacts on the freezing environment of the ground ice at the Taiga-Tundra boundary in northeastern Siberia. Such changes in the freezing environment will then affect vegetation due to changes in the microtopography of the ground surface.