To select the optimal site for the restoration of seagrass habitats in the Taehwa River estuary, we transplanted the eelgrass Zostera marina to three potential candidate sites in March 2007 and monitored the transplanted seagrass and associated environmental factors for six months. In all three sites, the transplanted seagrasses exhibited no initial morphological loss due to transplanting stress. The transplanted seagrass communities at sites 2 and 3 showed more than a 180% increase in density over the entire survey period. In contrast, despite a density increase in the first month after transplantation, most of the transplanted seagrasses at site 1 died. This may be due to the large decrease in underwater irradiance reaching the seagrass leaves at site 1 for two months during June and July, which fell below the level of compensation irradiance. The growth rate and size of the seagrass shoots were also larger at sites 2 and 3 compared with site 1. This is probably due to higher nutrient concentrations in the sediment pore water at sites 2 and 3 compared with site 1, although water depth, salinity, and the nutrient concentrations in the water columns from the three sites were similar. Therefore, for the restoration of seagrass habitats in the Taehwa River estuary, sites 2 and 3 were preferable to site 1 as transplantation sites.