The diatom oxygen isotope composition (δ18Odiatom) from lacustrine sediments helps tracing the hydrological and climate dynamics in individual lake catchments, and is generally linked to changes in temperature and δ18Olake. Lake Bolshoye Shchuchye (67°53′N; 66°19′ E; 186 m a.s.l) is the largest and deepest freshwater reservoir in the Polar Urals, Arctic Russia. The diatom oxygen isotope interpretation is supported by modern (isotope) hydrology, local bioindicators such as chironomids, isotope mass-balance modelling and a digital elevation model of the catchment. The Bolshoye Shchuchye δ18Odiatom record generally follows a decrease in summer insolation and the northern hemisphere (NH) temperature history. However, it displays exceptional, short-term variations exceeding 5‰, especially in Mid and Late Holocene. This centennial-scale variability occurs roughly contemporaneously with and similar in frequency to Holocene NH glacier advances. However, larger Holocene glacier advances in the Lake Bolshoye Shchuchye catchment are unknown and have not left any significant imprint on the lake sediment record. As Lake Bolshoye Shchuchye is deep and voluminous, about 30–50% of its volume needs to be exchanged with isotopically different water within decades to account for these shifts in the δ18Odiatom record. A plausible source of water with light isotope composition inflow is snow, known to be transported in surplus by snow redistribution from the windward to the leeward side of the Polar Urals. Here, we propose snow melt variability and associated influx changes being the dominant mechanism responsible for the observed short-term changes in the δ18Odiatom record. This is the first time such drastic, centennial-scale hydrological changes in a catchment have been identified in Holocene lacustrine diatom oxygen isotopes, which, for Lake Bolshoye Shchuchye, are interpreted as proxy for palaeo precipitation and, on millennial timescales, for summer temperatures.