On the example of estuary of the middle size boreal river Razdolnaya (Primorsky Krai, Russia) it is shown that even 5–6 times increase in the annual river runoff leads to the only 10–20% increase in the content of fine fractions in the surface 1–2 cm layer of bottom sediments, located within the outer part of the estuary –
the Amur Bay, Sea of Japan. The chemical composition of the sediments of the inner estuary, located within the river bed, is controlled mainly by variations of the grain size. In the outer estuary, pollution from Vladivostok city is an additional factor that upturns the content of Hg, Cd, Pb, Cu, Zn in the upper 30–35 cm layer of sediment. The concentration of Mo and Corg is also elevated in the sediments of outer estuary, but due to accumulation at the reductive diagenesis for Mo, and increased plankton production for Corg. It is possible to assess the vertical distribution in characteristics in the upper layer of estuarine sediments only taking into account the rate of sedimentation, which allows to highlight periods of anthropogenic pollution, as well as the effect of the dynamics of destruction of organic matter.