Zengwun estuary in Taiwan is a key habitat for the endangered black-faced spoonbill (Platalea minor), a piscivorous migratory bird. In the winters 2011-2012 and 2012-2013, the percentages were nearly half of that in 2007-2008 (65.5% and 51.1%). To find the reasons of the decline of the habitats is important for the preservation of the endangered bird. So, we used an unsupervised classification method to analyze high spatiotemporal satellite images from FORMOSAT-2 from 2004 to 2013, and found that the quality of spoonbill habitats has deteriorated. The deterioration mainly caused by many of the fishponds there, changing the raised fish from milkfish to grouper fish for the purpose of business benefit in recent 3 years. The water depth in the fishponds, which raised milkfish, used to be kept below 30 cm for the convenience in harvesting in winter. Besides, they left the uneconomical small fish behind in the ponds, which provided the black-faced spoonbills good places to forage. However, after the fishponds were changed to raise grouper fish, it not only made the small fish no more exist in the ponds, but also the developing engineering to deepen the fishponds made the trees around these ponds been cleaned. These trees could have provided shields for the black-faced spoonbills against chilly wind. As a consequence, these changes have substantially reduced the agreeable region where the depth of water should be less than 30cm for black-faced spoonbill to forage and inhabit. New reserves for spoonbills have been established recently in Taiwan. Nevertheless, a detailed plan for maintaining food resources for spoonbills as well as returning them habitats, must be implemented immediately.