The Lena River forms one of the largest deltas in the Arctic. We compare two sets of data to reveal new insights into the hydrological, hydrochemical, and geochemical processes within the delta: (i) long-term hydrometric observations at the Khabarova station at the head of the delta from 1951 to 2005; (ii) field hydrological and geochemical observations carried out within the delta since 2002. Periods with differing relative discharge and intensity of fluvial processes were identified from the long-term record of water and sediment discharge. Ice events during spring melt (high water) reconfigured branch channels and probably influenced sediment transport within the delta. Based on summer field measurements during 2005–2012 of discharge and sediment fluxes along main delta channels, both are increased between the apex and the front of the delta. This increase is to a great extent connected with an additional influx of water from tributaries, as well as an increase of suspended and dissolved material released from the ice complex. Summer concentrations of major ion and biogenic substances along the delta branches are partly explained by water sources within the delta, such as thawing ice complex waters, small Lena River branches and estuarine areas.