Several magnetic resonance soundings (MRS) in the Netherlands showed a monotonous single peak anomaly on the amplitude versus excitation moment sounding pattern, which were interpreted as a single aquifer when using an amplitude-only mode MRS data inversion. However, in all these soundings, borehole logs documented the presence of two or three aquifers separated by clay-rich aquitards in the first 100 m below ground surface. Such environments were electrically conductive so a phase excursion was noticeable on the MRS soundings. Multi-aquifer systems, in a conductive environment, may show interference among signals originating from different parts of the systems including amplitude masking or destructive interference. A new version of an off-the-shelf MRS forward modelling and inversion tool (Samovar 11.3) allowing complex amplitude and phase inversion was used to detect and parameterize deep, MRS-masked second aquifers at two selected sites in the Netherlands, one near Delft and one near Waalwijk. At the Delft site, the proposed strategy was effective in the detection and characterization of a second previously missed aquifer at 45 m below ground surface, while at the Waalwijk site, the second aquifer was not detected because of a considerably deeper aquifer at 85 m and too small excitation (6000 A ms). However, forward modelling showed that with a larger excitation moment (e.g., 13 000 A ms), detection and parameterization of the second aquifer would become possible when using both amplitude and phase.