Sediment cores were collected from one site each in Amursky and Ussuriysky Bays in the Peter the great Bay for $^{210}Pb$, org C, N, biogenic Si, ${delta}^{13}$C and ${delta}^{15}$N analysis to elucidate the processes of biogenic particulate matter accumulation and early diagenetic change in the upper sediment column. Biogeochemistry at the core sites of both bays shows differences in sedimentation rate, sediment mixing, and diagenetic processes of particulate biogenic matter. Sedimentary organic matter at the core sites in both bays appeared to be largely derived from marine origin. Sedimentation rates are 173 and 118 mg $cm^{-2}$ $yr^{-1}$(0.13 and 0.11 cm $yr^{-1}$) in Amursky and Ussuriysky Bays, respectively. The surface mixed layer in the core top was present in Amursky Bay but not in Ussuriysky Bay. At the core site in Amursky Bay, incorporation of biogenic particulate matter into the sediment from the overlying waters is 236, 19, 142 mmol $cm^{-2}$ $yr^{-1}$ for organic C, N, and biogenic Si, respectively. Of which about 70${\%}$ of organic C and biogenic Si are degraded within the upper 25 cm sediment and the rest are buried at 25 cm sediment horizon. At the core site in Ussuriysky Bay, incorporation of biogenic particulate matter into the sediment from overlying waters is 164, 18, 76 mmol $cm^{-2}$ $yr^{-1}$ for organic C, N, and biogenic Si, respectively. Of which less than 50${\%}$ of organic C and biogenic Si are degraded within the upper 25 cm sediment and the remainder are buried at 25 cm sediment horizon. This large difference of degradation of biogenic matter in the upper 25 cm sediment column appears to be resulted from the difference in sediment mixing rates between the two cores.