Effect of isotopic substitution on near-infrared (NIR) spectra has not been a subject of systematic studies. NIR spectra even relatively simple molecules are very complex, and therefore a detailed interpretation of spectral changes in this region is a challenging task. Recent progress in anharmonic quantum mechanical calculations allows for accurate simulation of NIR spectra. Here, we present a systematic study of the effect of isotopic substitution on NIR spectra of ethanol. To obtain a comprehensive understanding of NIR spectra we considered both different conformations (gauche, trans) and isotopologues (CX3CX2OX; X = H, D) of ethanol. The anharmonic calculations were based on generalized vibrational second-order perturbation theory (GVPT2) at DFT-B2PLYP/def2-TZVP level. Simulations included the first and second overtones, as well as binary and ternary combinations bands. This way we successfully reproduced even fine features in the spectra of diluted (0.1 M in CCl4) samples. Additionally, we demonstrated the potential of anharmonic calculations in predicting the spectra of the samples, which are not commercially available (CH3CD2OD and CD3CH2OD). Our results reveal complex nature of the changes in NIR spectra of ethanols due to coexistence of structural and isotopic effects.