Abstract To understand the origin of the nitrate anion selectivity in layered double hydroxide (LDH; [Ni1−xAlx(OH)2]Clx) materials (i.e., Cl−-NiAl(x)LDH; x = 1/3 and 1/5) comprising Ni2+, Al3+, and exchangeable chloride anions, the equilibrium and kinetic properties of the chloride-to-nitrate anion exchange reaction were investigated in aqueous media. The anion exchange isotherms of the studied systems showed that the nitrate anion selectivity was significantly higher at x = 1/5 than at x = 1/3. The fine crystal structures of the LDH materials and the hydration states of the nitrate anions in their interlayer spaces were identified by synchrotron-radiation X-ray diffraction (SXRD) and Raman spectroscopy, respectively. The nitrate anion selectivities of Cl−-NiAl(x)LDH (x = 1/3 and 1/5) were determined by the relationship between the magnitudes of the thermal vibration parameters of the chloride and nitrate anions; the anion exchange reaction primarily gave NiAl(x)LDH containing anions with smaller thermal vibration parameters. Time-resolved SXRD measurements of the anion exchange reaction revealed that the exchange pathway differed depending on the nitrate anion selectivity. The nitrate anion removal ability and selectivity of Cl−-NiAl(x)LDH (x = 1/3 and 1/5) in artificial seawater were maintained, suggesting that Cl−-NiAl(1/5)LDH could be used for nitrate removal from contaminated seawater.