Neurochemical concentrations determined by magnetic resonance spectroscopy (MRS) have been treated as statistically independent measurements in various clinical MRS studies. However, spectral overlap, independent of any biological effects, could lead to significant correlations between neurochemical concentrations extracted from spectral fitting of MRS data, confounding determination of correlations of biological origin. Short echo time (TE) proton MRS spectra are very crowded because of the comparatively narrow chemical shift dispersion of proton nuclear spins. In this study, the complex neurochemical correlations of spectral origin in short‐TE MRS spectra were quantified. The effects of macromolecules and the background spectral baseline on metabolite–metabolite correlations were also analyzed. Our results demonstrate the importance of factoring in spectral correlations when correlating overlapping metabolite signals in short‐TE spectra with clinical parameters.