Changes in the lower-trophic marine ecosystem and biogeochemical cycles were considered with respect to the warming Arctic Ocean. The time series monitoring of the hydrography and marine settling particles supplies a large amount of information regarding the marine lower-trophic ecosystem in with respect to the changing Arctic Ocean. To investigate the interannual relationship between the settling particles and hydrographic conditions of the western Arctic Ocean, bottom-tethered sediment trap moorings were deployed at the Northwind Abyssal Plain (NAP) and at the Chukchi Abyssal Plain from October 2010 to September 2014 to the east and west of the Chukchi Borderland. The settling particles at both stations contained a significant amount of lithogenic matter, with biogenic particles being a lateral advection of shelf materials from shelf to basin. The many peaks of settling particle fluxes at Station NAP in 2013–2014 corresponded to the hydrographic events of passing oceanic eddies over the station, in addition to seasonal biological production. Additionally, abundant gelatinous matter was found in some summer samples. The settling flux data of particulate organic matter and the mole ratio and stable isotope ratios of particulate organic carbon and nitrogen in the settling particles reflected the changes in the composition of trapped plankton assemblages under various hydrographic conditions over the course of the four years of the study.