The pathways of fluids and mantle-originated carbon dioxide in the seismically active Ohře (Eger) Rift system appearing as mofettes at the surface are currently subject to investigation, especially by the International Continental Scientific Drilling Program “Drilling the Eger Rift”. If the aquifers show significant contrast in electrical resistivity to the host rocks, they can be investigated with geo-electromagnetic methods. However, imaging complex fluid and CO2 pathways in detail in near-surface structures is challenging, because, in contrast to the background stratigraphy, they are often oriented in near-vertical directions. Therefore, we aim to investigate how the shallow aquifer structures can be examined best with an inductive electromagnetic method. For this purpose, we collected radio-magnetotelluric data in the Hartoušov mofette field and evaluated them by two- and three-dimensional inversions. Data from a nearby magnetotelluric station, drill hole data, gas flux measurements and electrical resistivity tomography models were used to assess the reliability and robustness of our inversion results. We concluded that the near-surface fluid reservoirs are adequately depictable, while the migration paths of gaseous CO2 cannot be traced properly due to a lack of resistivity contrast. Our model analyses suggest that imaging the given geological setting with fluids and gases ascending in anastomosing pathways benefits from a fine-scale three-dimensional inversion approach because the fluids mostly appear as local conductive reservoir-like anomalies, which can be falsely projected onto the profiles during inversion in two dimensions. The resistivity models contribute with detailed images of the near-surface aquifers to the geodynamic model of the Ohře Rift.