Past temperature reconstructions from polar ice sheets are commonly based on stable water isotope records in ice-cores. However, despite major efforts in the understanding of the ice-core signal formation, the temperature reconstructions of the last millennium in Antarctica remain highly uncertain. Here, using a 100 km scale representative surface water isotope dataset, we show that the spatial variability of local surface topography and accumulation rate anomalies influences the isotopic composition of the upper-meter snowpack. The magnitude of this non-temperature effect on water isotopes is similar to changes of the last millennium. We demonstrate that these spatial anomalies are advected into the deeper firn and ice column, and are translated into an artificial centennial to millennial scale variability in the isotope record. Additionally, we provide an estimation of areas where this effect is relevant for last millennium temperature reconstructions.