We used two different loop-loop electromagnetic induction (EMI) devices to determine the 3D geometry and morphology of the pedo-sedimentary filling and underlying basaltic bedrock of a former wetland in a volcanic soil area, the Lac du Puy depression (Auvergne, France). Electrical conductivity (or resistivity) is usually sufficient for environmental and soil science applications, but the local volcanic context of the survey area results in high values of magnetic susceptibility and possible electrical polarization effects. Therefore we investigated the roles of the four properties: electrical conductivity, magnetic susceptibility, magnetic viscosity and dielectric permittivity. We created models using these four properties for the two coil configurations of each device in order to assess the degree to which each of the properties contributed to the recorded electromagnetic signal. The results show that electrical conductivity controls the quadrature component of the secondary field response but that it can be affected by high values of magnetic viscosity, while magnetic susceptibility controls the in-phase component. Moreover, the low frequencies imply a limited contribution of dielectric permittivity to the in-phase component, except in the cases of higher permittivity or frequency values or greater inter-coil separation. Based on these observations, we propose a way to map the apparent properties from field measurements. We then carried out a 1D inversion, first by considering the electrical conductivity alone and secondly by taking all the electromagnetic properties into account. The results show that there is a marked contrast in the complex magnetic susceptibility between the sedimentary in-fill and the border of the Lac de Puy depression, (stronger than for the electrical conductivity), and that permittivity is unlikely to have a significant influence. The shape and nature of the sedimentary in-fill was thus considerably refined by the second inversion results based on the three other properties. These data, combined with litho-stratigraphic observations from a previous study, allowed the lateral continuity and geometry of the in-fill to be assessed across the whole basin. Results are also consistent with previous interpretations of the depression as a pseudo-sinkhole, a relatively common morphology in volcanic plateaus. Analysis of the magnetic properties also made it possible to characterize the spatial variation of some key features related to hydromorphic processes, such as clayey granularity and the development of iron oxides/hydroxides. This opens up the possibility for using new methods for rapid spatial and pedological characterization of hydromorphic soils and palaeosoils.