Paleoecology is a powerful tool to reconstruct the long-term history of marine ecosystems. Here, we show an example of how paleoecology can help to investigate a natural-baseline biological community before anthropogenic environmental modification. Plover Cove Reservoir, located in northeastern Hong Kong, was the world's first successful trial to construct a freshwater lake by building dams in a marine inlet during the 1960s. Multiproxy analyses including sedimentology, ostracodes, foraminifera, macrofossils, and organic geochemistry were conducted on a sediment core to reveal the aquatic benthic community history during this major environmental change. Before the reservoir construction, a rich and diverse shallow muddy inner-bay community was distributed throughout the inlet. During the construction period, the area became uninhabitable due to damming and drainage, except for a small number of individuals of a few marginal marine ostracode species that can endure eutrophicated and intertidal habitats. After the completion of the freshwater reservoir, the benthic habitat was left barren when the bottom water became anoxic.