Long-term ecological research is imperative for comprehensively understanding how ecosystems respond to environmental changes over time. This study examined the long-term responses of seagrasses (Zostera japonica, Z. marina, and Z caespitosa) in intertidal and subtidal zones to anthropogenic disturbances and sea warming on the southern coast of the Korean peninsula over 15 years (2008–2022). Dramatic declines in the intertidal seagrasses were observed due to human activities such as clam harvesting and oyster cultivation, resulting in the disappearance of almost all Z. japonica in intertidal zones. Subtidal seagrasses, including Z. marina and Z. caespitosa decreased gradually throughout the study period. The biomass and canopy height of the subtidal Z. marina showed an inverse trend against water temperature. In addition, water temperature anomalies such as marine heat waves (MHWs) caused abrupt declines of seagrasses within both the intertidal and subtidal zones. Annually repeated and acute human-induced disturbances were the primary threat to the intertidal seagrass species. Nevertheless, the subtidal seagrasses were primarily affected by unpredictable summer MHWs as well as gradual rising water temperatures, with MHWs causing more dramatic alterations in the coastal seagrass ecosystems compared to gradual SST rising. The continuous decline of seagrasses due to natural and human-induced disturbances will alter the structure of shallow coastal ecosystems, leading to significant changes in the ecosystem services they provide. The results of this study underscore the importance of management actions in coastal seagrass ecosystems and highlight the need to predict future impacts of ongoing climate change.