A fish community in Hong Kong that had experienced megascale reclamation in Chek Lap Kok International Airport, and the ensuing marine protected areas (MPAs) establishment was tracked for 12 years. Significant shifts in community structure, typified by 17 species, were revealed by multivariate analyses and community metrics. Dynamic factor analysis disclosed two underlying common trends among them and their significant correlations with changes in water quality, area of seabed disturbance, and area of MPAs. A time-lag for detectable community changes was also revealed. During reclamation, the fish density was low and community health was poor. Large species disappeared leaving a community dominated by small, fast-growing and young-to-mature species. After completion of reclamation, some large and medium species returned, but soon after the establishment of MPAs, medium-sized, fast-growing and young-to-mature species thrived on reduction of fishing pressure, and filled the guilds rapidly. Therefore, even though fish density and community health were improved, the original community structure was not restored. This study provides a good reference for impacts of reclamation at the community level and the possible outcomes of reducing fishing pressure in a depleted fish community.