Coastal wetlands are important ecosystems because of their high biological productivity and role as habitat for wildlife, shoreline protection from erosion, pollutant removal and bioremediation, and water quality purify. The agricultural waste discharged into the coastal wetlands led to coastal pollution in the intertidal zone at Fangyuan area in Taiwan. Twelve sampling sites were monitored during the study period from June 2006 to May 2007 in Fangyuan mangrove wetland. The establishment of Habitat Assessment Procedure (HEP) for Fangyuan mangrove wetland. Bioremediation of polluted habitat enhancement to create a reference in the biological diversity concept. The results showed that pH, total phosphorus (TP), sediment pH, total organic matter and sediment oxygen consumption have important influencing factors by HSI.