We examined whether replantation of benthic microalgae (BMA) can remediate shallow organically enriched sediment. Nitzschia sp., the dominant species in the tested area (Hiroshima Bay, Japan), was isolated and mass cultured, then replanted in the same area. Changes in the condition of the sediment were monitored for five months. During the study period, we observed an increase in redox potential (ORP) and a decrease in acid-volatile sulfide (AVS) in the experimental area, indicating that the sediment condition changed from reduced to oxic. Organic matter in the sediment, represented by chemical oxygen demand (COD), ignition loss (IL) and organic nitrogen (ON), decreased significantly, while inorganic nutrients (ammonia and phosphate) increased in the interstitial water. These changes imply that oxygen produced by the replanted BMA may have enhanced aerobic bacterial activity, accelerating the decomposition of organic matter. Thus, replantation of BMA shows potential as a novel and promising "phytoremediation" method for organically enriched sediment.