This paper aims to investigate the magnetic resonance signal generated by shallow aquifers and its influence on the interpretation of magnetic resonance sounding (MRS) data. To improve the accuracy of MRS modelling in the presence of shallow aquifers, an enhanced mathematical model, which takes into account the higher harmonics of the transmitted pulse and a non-zero frequency offset between the Larmor frequency and the pulse frequency, is used. It is shown that in the presence of shallow aquifers, the magnetic resonance signal is complex even when the subsurface has a low electrical conductivity. At large pulse moments, water in shallow aquifers may generate a signal comparable in amplitude to a signal generated by water in deeper aquifers. Two types of error related to a shallow aquifer may occur. For a one-aquifer system, interpretation using the simplified model may reveal an artefact that appears to be a deeper aquifer, although in reality it is non-existent (a phantom aquifer). For a multi-aquifer system, the signal from a shallow aquifer may offset the signal from a deeper aquifer, thus reducing the depth of investigation in comparison with a simple one-aquifer formation (offset of a deep aquifer). It is shown numerically that the depth resolution of the MRS method could be significantly improved by considering not only the amplitude but also the phase of the MRS signal. However, taking into account the non-linearity of the spin system for a large flip angle, the mathematical model for the inversion of complex signals needs to be further improved or at least checked for consistency before inversion. For verification of the numerical results, a re-interpretation of MRS field data reported in the literature is presented.