Previous studies have found EEG amplitude and scalp topography differences between neurotypical and neurological/neurosurgical groups, being interpreted at the cognitive level. However, these comparisons are invariably accompanied by anatomical changes. Critical to EEG are the so-called volume currents, which are affected by the spatial distribution of the different tissues in the head. We investigated the effect of CSF-filled cavities on simulated EEG scalp data. We simulated EEG scalp potentials for known sources using different volume conduction models: a reference model (i.e., unlesioned brain) and models with realistic CSF-filled cavities gradually increasing in size. We used this approach for a single source close or far from the CSF-lesion cavity, and for a scenario with a distributed configuration of sources (i.e., a cognitive ERP effect). Magnitude and topography error between the reference and lesion models were quantified. For the single-source simulation close to the lesion, the CSF-filled lesion modulated signal amplitude with more than 17% magnitude error, and topography with more than 9% topographical error. Negligible modulation was found for the single source far from the lesion. For the multi-source simulations of the cognitive effect, the CSF-filled lesion modulated signal amplitude with more than 6% magnitude error, and topography with more than 16% topography error in a non-monotonic fashion. In conclusion, the impact of a CSF-filled cavity cannot be neglected for scalp-level EEG data. Especially when group-level comparisons are made, any scalp-level attenuated, aberrant, or absent effects are difficult to interpret without considering the confounding effect of CSF.