Time‐domain marine controlled source electromagnetic methods have been used successfully for the detection of resistive targets such as hydrocarbons, gas hydrate, or marine groundwater aquifers. As the application of time‐domain marine controlled source electromagnetic methods increases, surveys in areas with a strong seabed topography are inevitable. In these cases, an important question is whether bathymetry information should be included in the interpretation of the measured electromagnetic field or not. Since multi‐dimensional inversion is still not common in time‐domain marine controlled source electromagnetic methods, bathymetry effects on the 1D inversion of single‐offset and multi‐offset joint inversions of time‐domain controlled source electromagnetic methods data are investigated. We firstly used an adaptive finite element algorithm to calculate the time‐domain controlled source electromagnetic methods responses of 2D resistivity models with seafloor topography. Then, 1D inversions are applied on the synthetic data derived from marine resistivity models, including the topography in order to study the possible topography effects on the 1D interpretation. To evaluate the effects of topography with various steepness, the slope angle of the seabed topography is varied in the synthetic modelling studies for deep water (air interaction is absent or very weak) and shallow water (air interaction is dominant), respectively. Several different patterns of measuring configurations are considered, such as the systems adopting nodal receivers and the bottom‐towed system. According to the modelling results for deep water when air interaction is absent, the 2D topography can distort the measured electric field. The distortion of the data increases gradually with the enlarging of the topography's slope angle. In our test, depending on the configuration, the seabed topography does not affect the 1D interpretation significantly if the slope angle is less or around 10°. However, if the slope angle increases to 30° or more, it is possible that significant artificial layers occur in inversion results and lead to a wrong interpretation. In a shallow water environment with seabed topography, where the air interaction dominates, it is possible to uncover the true subsurface resistivity structure if the water depth for the 1D inversion is properly chosen. In our synthetic modelling, this scheme can always present a satisfactory data fit in the 1D inversion if only one offset is used in the inversion process. However, the determination of the optimal water depth for a multi‐offset joint inversion is challenging due to the various air interaction for different offsets.