The springs of Jeju Island have been studied since 1999. However, previous studies did not provide a systematic analysis of survey results. Thus, we performed a systematic analysis of the groundwater flow system using cluster analysis of discharge variables, i.e., discharge rate, electrical conductivity (EC), and temperature, at 121 springs. The 121 springs were categorized into nine major groups based on discharge rates and ten groups based on EC. Springs in groups 1, 2, and 3 in discharge cases had peak discharge rates in September, October, and occasionally in November, following the rainy season. Other springs showed complex seasonal variation in discharge rates. Springs in groups 4–1, 4–3, 5–2, 9–1, and 9–2 had peak discharge rates in winter (December–February). The results of classification by EC were directly correlated with the absolute values of and seasonal variation in EC. Based on EC, springs in group 1 had relatively low EC of > 500 μS/cm in general. The highest EC at each spring in group 1 was 110–18,000 μS/cm. Coastal springs generally had higher EC than did springs located inland. The relation between discharge rate and EC was of interest. At some springs, discharge rate and EC were proportional, especially in winter. The proportionality between discharge and EC cannot be explained by the conventional groundwater management model of Jeju Island. To explain this proportionality, we examined the results of previous studies with regard to geological features, well locations, hydraulic head and hydraulic gradient distributions, and vertical reduction in groundwater EC within the zone influenced by saline water. We then proposed a hypothetical regional conceptual model of groundwater flow for Jeju Island. More precise studies are needed to clarify the relationships among responses at surveyed springs, hydraulic features in coastal areas, and the regional conceptual model for groundwater circulation on Jeju Island.