Verifying the similarity of environmental characteristics between an artificial impact site and a preserved or reference site is necessary to quantitatively and qualitatively evaluate the environmental impact of mining activity. Although an impact site (BIS station) and a preserved site (called KOMO station) that have been selected in the Korea manganese nodule contract area may share similar environmental characteristics, similarities in terms of the water column environment between both sites has not been investigated. In this study, we compared the chemical properties of the water columns and sinking particle fluxes between BIS and KOMO stations through two observations (August 2011 and September 2012). Additionally, we observed particle fluxes at the KOMO station for five years (July 2003~July 2008) to understand long-term natural variability. Vertical distributions of water column properties such as dissolved oxygen, inorganic nutrients (N, P, Si), total organic carbon below surface layer (within the depth range of 200 m) were not considerably different between the two sites. Especially, values of water column parameters in the abyssopelagic zone from 4000 m to bottom layer (~5000 m) were very similar between the BIS and KOMO sites. Sinking particle fluxes from the two sites also showed similar seasonality. However, natural variation of particle flux at the KOMO site varied from 3.5 to $129.9mg;m^{-2}day^{-1}$, with a distinct temporal variation originating from ENSO events (almost forty times higher than a minimum value). These results could provide valuable information to more exactly evaluate the environmental impact of mining activity on water columns.