With over-extraction of groundwater, excess fluoride greater than 1.5mg/L (i.e. WHO standard) exposed to people, causing severe environmental and health problems. Interaction of fluoride and calcium carbonates is of importance in controlling the groundwater quality in Karst area with abundant limestone present. However, little is known about the reactivity and stability of fluoride with carbonates owning to the lack of molecular scale characterizations. In this study, we employed ¹⁹F solid-state nuclear magnetic resonance (NMR) spectroscopy to investigate the local molecular-scale environment of fluoride after reacted with calcite. At low F concentration (≤1mM, at pH8), we observed a single ¹⁹F NMR peak at -122 ppm; at high F concentration (≥2mM, at pH8), the ¹⁹F NMR spectra yield two peaks at -108 and -122 ppm, respectively. This indicates two different reaction products; the -108 ppm peak could be assigned to fluorite (CaF₂), whereas the other peak at -122 ppm with FWHM of about 3 ppm were tentatively assigned to fluoride diffused or incorporated into calcite structure, which was further confirmed using Nano Secondary Ion Mass Spectrometer (NanoSIMS). Furthermore, High Resolution Transmission Electron Microscopy (HRTEM) equipped with Selected Area Electron Diffraction (SAED) characterization suggested the presence of a newly formed phase with distinct SAED pattern from that of calcite. Based on these results, a pseudomorphic replacement model can be proposed for interpreting F/calcite interaction, which are essential to understand the surficial interaction between anions and calcite and access the vulnerability of groundwater in carbonated layers (e.g. Karst).