Inversion of electromagnetic sub-bottom parameters and 3D modelling of the bottom topography is presented in this paper. In particular, horizontally stratified conductivity profiles are determined from space- and frequency-sounding data collected at a controlled electromagnetic (CEM) source experiment in the southern Stockholm archipelago conducted in June 2004. The inversion, of the piecewise continuous conductivity profiles, is formulated as an optimisation problem. A restarted local Levenberg-Marquardt search algorithm is used to determine the sub-bottom conductivity profile that minimises the differences between measured and numerical data. The obtained results, for a specific part of the trial site, are compared with inverted profiles from a similar field trial performed in August 2002 in the same area. Especially, the impact from the seasonal variation in the seawater conductivity profile on the estimated sub-bottom profiles is indicated. Finally, effects from the bottom topography on the electric field when a source is towed along a track are inverstigated and modelled. A volume integral equation technique is used to model the non-planar part of the track. It is shown that the variations in the electric field amplitude due to different water depths along the track can be accurately modelled by using an extended Born approximation approach. The electric field amplitude is increased as much as 14 dB compared to a horizontally stratified bottom at the most shallow part of the track. Hence, the detection capability for an electric sensor system is increased when sources passes shallow parts of an area or close to island.