Layered double hydroxides (LDHs) are anion exchangers with a strong potential to scavenge anionic contaminants in aquatic environments. Here, the uptake of selenite (SeO32-) by Ca-Al LDHs was investigated as a function of Se concentration. Thermodynamic modeling of batch sorption isotherms shows that the formation of SeO32--intercalated AFm (hydrated calcium aluminate monosubstituent) phase, AFm-SeO3, is the dominant mechanism controlling the retention of Se at medium loadings. AFm-Cl2 shows much stronger affinity and larger distribution ratio (Rd ∼ 17800 L kg-1) toward SeO32- than AFm-SO4 (Rd ∼ 705 L kg-1). At stoichiometric SeO32- loading for anion exchange, the newly formed AFm-SeO3 phase results in two basal spacing, i.e., 9.93 ± 0.06 Å and ∼11.03 ± 0.03 Å. Extended X-ray absorption fine structure (EXAFS) spectra indicate that the intercalated SeO32- forms inner-sphere complexes with the Ca-Al-O layers. In situ X-ray diffraction (XRD) shows that basal spacing of Ca-Al LDHs have a remarkable linear relationship with the size of hydrated intercalated anions (i.e., Cl-, SO42-, MoO42-, and SeO32-). Contrary to AFm-SeO3 with inner-sphere SeO32- complexes in the interlayer, the phase with hydrogen-bonded inner-sphere complexed SeO32- is kinetically favored but thermodynamically unstable. This work offers new insights about the determination of intercalated anion coordination geometries via XRD analyses.