Mangrove degradation is a well-documented trend, but the spread of mangroves within the Siangshan Wetland in Hsinchu, Taiwan, runs contrary to that trend. The spread of mangroves changes the structure and functions of habitats for benthic organisms, causes infilling of estuaries and flooding and creates breeding grounds for small black mosquitoes. A large-scale mangrove-removal project was undertaken by the Hsinchu City Government from October 2015 to March 2016. They also investigated the consequences of mangrove removal on benthic organisms and adjacent habitats from October 2015 to September 2016, and the density, species count, Shannon–Wiener index (H′), and Pielou’s evenness index (J′) of the mangrove and non-mangrove regions were compared. In this study, we used satellite telemetry images to monitor fluctuations in mangrove density from 2006 to 2016. The non-mangrove region exhibited more variations than the mangrove region. After mangrove removal, species returned to their original habitats and noteworthy biological values significantly increased in the mangrove regions. This study presents evidence to argue that mangrove removal benefits benthic organisms. The results indicate that mangrove removal can be an appropriate habitat rehabilitation strategy for benthic organisms. The ecological findings of this study can inform coastal managers or other officials who seek to steward mangrove biomass.