The groundwater characteristics in two areas, Tushan town (TS) in Laizhou County and Puzhuang town (PZ) in Changyi County, were compared to discuss the dynamics of fluorine enrichment. Groundwater has average fluorine levels of 2.33 mg/L in PZ town ranging from 0.65 to 9.87 mg/L and of 0.91 mg/L ranging from 0.27 to 1.25 mg/L in TS town. The geochemical indexes indicate seawater intrusion in the both areas, the more serious seawater intrusion in PZ town causes the higher pH, electrical conductivity (EC), total dissolved solids (TDS), HCO3− and Na+ than TS town, which can accelerate fluorine leach ability from rock/soil and result in higher fluorine than in TS town. So, the seawater intrusion is related to groundwater fluorine levels. Moreover, the groundwater shows the contrary process of cation exchange. That is, the exchange of Na+ to Ca2+ in TS town occurs and that of Ca2+ to Na+ occurs in PZ town during seawater intrusion. As a result, PZ town has relatively higher Na+ and lower Ca2+ than TS town, and the groundwater types transform from Ca-Cl type in TS town to Na-Cl type in PZ town with the ongoing seawater intrusion. Such a process decreases fluorine solubility in groundwater and contributes to lower fluorine levels in TS town. Therefore, the seawater intrusion and the special cation exchange explain well the different fluorine levels in the two areas, which should be considered when the fluorine enrichment is discussed in coastal regions.