AbstractWe studied the influence of river discharge and timing of ice retreat on sinking fluxes of total particulate matter and its components in the Laptev Sea in August–September 2017 and 2018. Vertical fluxes were measured with short‐term sediment traps located on the shelf adjusted to the Lena and Khatanga Rivers inflows (four shallow stations in 2017) and in Vilkitski Strait/Trough area (two deeper stations) in 2018. One station outside the Khatanga plume was repeated in both years. The effect of river discharge manifested by high total particle flux (1–1.6 g m−2 d−1), high Si (0.3 g m−2 d−1) and Al (0.1 g m−2 d−1) fluxes, a high proportion of terrigenous organic carbon (10.7%–27.5% total organic carbon) was clearly recognizable only in the shelf area closest to the Lena inflow. Large contribution of the lithogenic matter to the flux on the Laptev shelf is suggested to result also from sediment resuspension (caused by the tidal mixing and upwelling events), lateral offshore transport of sediment just above the seabed, and coastal abrasion. The magnitude of vertical fluxes of total particulate matter and organic carbon was two to three times higher in 2017 (late ice retreat) than in 2018 (early ice retreat). Centric diatoms dominated protist flux in 2017 while in 2018, dinoflagellates and tintinnids dominated. The contribution of protists to the biogenic organic carbon flux reached 62% in 2018 versus <1% in 2017. Zooplankton fecal pellet flux was not influenced by river discharge but was higher soon after ice melt.