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 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 comparable to the changes observed over the last millennium. We demonstrate that these spatial anomalies are advected into the deeper firn and ice column, and can explain the diverging millennial water isotope trends observed in two ice-cores near the EPICA Dronning Maud Land drilling site. Furthermore, we provide an estimation of areas where this topographic effect could impact temperature reconstructions over the last millenia.