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In the last 30–40 years, the flux of the Lena River have undergone significant changes due to, mainly, climatic factors. Features of these changes at the marine margin of the Lena delta are different compared to changes in the basin outlet station. The reason is transformation of runoff in the large and multi-branched delta. The water runoff in the lower reaches of the Lena River has increased due to all hydrological seasons by 41.7 km3 per year (in 1980–2014 vs 1935–1979), the suspended sediment load – by 5.85 mln tons per year (since 1988), the heat flux – by 0.8•1015 kJ/year. An increase in water temperature has been noted as well. The main increase in flux has been observed since the end of the 1980s. The water use had almost no impact on the water resources of the river, but have violated natural conditions of winter low water. In the main delta branch node the percentage of water runoff of the Bykovskaya branch was about 25%, Trofimovskaya – 61%, Tumatskaya – ~ 7%, Olenekskaya – 7%. Within a year, these ratios change. The suspended sediment load: 17, 70, 7 and 6%. The runoff to the sea is distributed between ~6 thousand streams and is rather unstable due to the fluviomorphological processes. The water runoff at the basin outlet station, delta head and marine margin equals to 543, 547 and 553 km3/year; suspended load is roughly 22.5, 22.5 and 7.9–13.5 million tons. The research has been performed at the expense of RSF Grant 14-37-00038.