Groundwater systems in coastal aquifers may be affected by sea level change as increased seawater intrusion occurs with sea level rise. Artificial pumping taking place at the same time will increase this impact. In order to estimate the vulnerability of groundwater systems with sea level rise within coastal aquifers in South Korea, long-term groundwater data were analyzed using basic statistics, trend analysis, and correlation analysis. Conductivity depth profiling was also periodically conducted. Groundwater levels increased in wells with relatively low groundwater elevations but decreased in wells with higher groundwater elevations. At the same time, conductivity variations were greater in wells located in reclaimed land areas, which vertical conductivity profiles indicated were more affected by sea level variations, but decreased on the mainland. Results of auto-correlation analysis showed a decreasing trend with cyclic variations and significant periodic patterns during dry seasons, indicating that groundwater levels were not affected by artificial factors and that those in reclaimed land areas were less affected by rainfall than on the mainland. These results coincided with those from cross-correlation analysis showing that groundwater level was affected by sea level variation during the dry season. Sea level changes, which may be related to climate change, as well as rainfall in South Korea can influence groundwater levels, and the groundwater system in reclaimed land areas may be more affected than on the mainland, especially under dry conditions.