Land-shelf interactions and related environmental changes were reconstructed for the past 6 cal. kyrs interpreting multiproxy records from the two AMS14C-dated sediment cores from the sites located to the north and northeast of the Lena River delta. Proxies used include terrestrial and aquatic palynomorphs, benthic/planktic foraminifers and ostracods paired with benthic δ18O and δ13C records of Haynesina orbiculare. The study focused on unravelling the relation between river runoff and the regional climate changes on the one hand, and its imprint on the shelf sea environment on timescales beyond the instrumental records on the other. The palynomorph records show that the Lena River outflow largely determined the composition of species associations and the magnitude of terrestrial matter influx from land. Pollen assemblages of the inner Laptev Sea shelf reflect complex pollen contribution of the Arctic tundra and remote taiga zones drained by the Lena River and indicate a vegetation response to warmer-than-present climatic conditions between 6.0 and 4.5 cal. ka and a subsequent gradual cooling. Fluvial influence in the records is manifested by (1) increases in sedimentation rates; (2) high influxes of pollen/spores and freshwater chlorophycean algae, wood and plant remains; (3) negative δ13C excursions due to the introduction of dissolved inorganic carbon (DIC) from river water. Episodes of enhanced freshwater influence in the surface water layers (fluvial events) correlate with positive benthic δ18O excursions and increasing representation of river-distal species among benthics. Altogether, this points to an estuarine-like reversed (north to south) bottom current activity along the submarine paleovalleys on the shelf. The most pronounced fluvial events are recognized at 5.3–5.9, 1.5 and <0.5 cal. ka. The oldest fluvial event coincides with the final stage of mid-Holocene climate warming. A fluvial event at 1.5 cal. ka is specifically strong at the northeastern site thus marking a direction change of the Lena River outflow at this time and the progressive protrusion of the delta. During the past 500 years distinct negative δ13C values at the northeastern site reflect enhanced riverine influence. It is therefore concluded that the unprecedented change in the δ13C trend corroborates the other evidence for a principal diversion of the major Lena River outflows into its present-day, easterly direction.