Human impacts cause significant problems for shallow lakes in the karst regions of South China. In recent years, the ecological issues related to managing and restoring these critical aquatic ecosystems have come to the fore. Lingshui Pool (LSP) is one of the most-studied spring-fed lake ecosystems in south China, and it has well-preserved chronological profiles. The LSP was a very shallow lake before dam construction in 1962. Due to the dam’s construction, rapid development and urbanization, this important freshwater ecosystem has suffered severe eutrophication and environmental degradation. In order to determine the environmental effects of recent anthropogenic disturbances and establish conservation recommendations for this lake ecosystem, we analyzed diatoms and weak-acid leachable elements from a well-dated sediment core from LSP to reconstruct the changes in aquatic conditions and diatom diversity during the period AD 1960–2013. This revealed shifts in diatom assemblages, diversity, and geochemistry that were strongly linked to the construction of a dam in 1962 and rapid eutrophication after 1990. Diatom diversity was stable and relatively high when submerged macrophytes were present between 1962 and 1990. Thus, the reintroduction of endemic macrophytes could benefit the ecological stability and diversity of this shallow lake.