Site-selective time-resolved laser spectroscopy techniques, which provide high spectral resolution at low temperatures (4.2 K and 6.5 K), were used to clarify the formation mechanism, spectral and kinetic properties of the Nd3+ ion single-site optical centers formed in the fluorite-type BaF2 single crystals doped with Nd3+. This formation occurs by heterovalent substitution of Ba2+ host cations with additional charge compensation by F− anions. To determine the lifetimes of the Stark 4F3/2(1) levels of the Nd3+ impurity centers, the fluorescence decay kinetics was measured using the gated photon counting technique. The data from spectroscopic experiments were combined with density functional theory (DFT) calculations to identify and analyze the local structure of Nd3+ cations in the Nd3+ ions doped BaF2 crystal. Our studies have shown that several types of single-site Nd3+ optical centers can be distinguished in BaF2:Nd3+. We confirmed the existence of an optical center with high C4v site symmetry and a long radiative lifetime of the 4F3/2(1) state τ = 14.3 ms. We also describe two other configurations of centers with local structure characterized by low site symmetry of Cs, which were identified and described for the first time. The decrease in the tetragonal site symmetry from C4v to Cs was explained by the fact that the Nd3+ dopants, distributed over the equivalent cationic positions of the fluorite-type crystal lattice, coordinate to anionic motifs that essentially differ in the position of the additional charge compensator F−. This structural variability induced in the local coordination environment of the optical center affects its spectroscopic properties through a shift in the energy of the 4F3/2(1) Stark level of the Nd3+ ion and results in a different radiative lifetime τ.