The process of increasing the capacity of the Russian Arctic harbors has been gaining momentum in recent years due to the environmental change associated with the global warming process and increasing role of the Northern Sea Route (NSR). An important component of this process is the operation of the Sabetta seaport in the Ob Bay, Kara Sea, intended for the transportation of hydrocarbons (oil and gas products) produced on the Yamal Peninsula in the NSR. The construction project of the Sabetta seaport includes the regular dredging to ensure navigational depths in the approach channels, and in the port at the piers. The regular dredging work can cause negative stress effects on water bioresources (fish) and thereby increase the risks of environmental management for coastal eco-socio-economic system. The total volume of planned annual dredging is 2554.4 thousand cubic meters of dredging material. To reduce risks, it is necessary to carry out environmental control measures for dredging operations, including determining of possible damage and developing compensatory measures that reduce negative effects and contribute to the restoration of biological resources. The paper provides an assessment of possible impacts on aquatic bioresources from dredging in the waters of the Sabetta seaport in the period from 2018 to 2027 and determines the amount of costs for environmental protection measures and compensation payments. The projected amount of damage to water biological resources during the dredging operation will be 176 tons of fish per year. It is shown that the most significant expression of the anthropogenic risk, associated with the implementation of dredging in the aquatory of the Sabetta seaport, will be decrease of biomass of biological bottom communities (zoobenthos). As a result of that, the decrease in bottom-feeding fish stocks is expected, but this process will be temporary. The estimated amount of expenses for compensation measures for three proposed fish species - objects of reproduction of yearlings for 1 year – will be: for peled C.peled – 64.82 million rubles, for Siberian sturgeon – 139.03 million rubles, for muksun C.muksun – 98.03 million rubles. To minimize this risk of environmental management, a number of environmental measures are proposed that will allow the Sabetta seaport to maintain its status as the first environmentally friendly port in the Russian Arctic.