The generation of short-period multiples between highly heterogeneous layers of basalt flows can strongly alter transmitted seismic wavefields. These layers filter and modify penetrating waves, producing apparent attenuation and phase changes in the observed waveforms. We investigated the waveform and apparent phase changes of the primary seismic signal using mainly the maximum kurtosis approach. We compared the seismic recordings from two short-offset vertical seismic profiles (VSPs) with synthetic seismograms, generated from sonic logs in the same wells, and we found that short-period multiples cause a rapid broadening of the primary arrivals and strong apparent phase changes within a short depth interval below the top of the basalt flows. Relatively large uncertainties were associated with estimating constant phase shifts of the seismic arrivals within the topmost 250 m of the basalt sequences, where complex scattering occurred. Within this interval of the Brugdan I well, a phase-only compensation of the first arrivals with a frequency-independent, combined scattering, and intrinsic attenuation operator was unfeasible. At a greater depth, we found that the phase shifts, predicted by a VSP-derived effective value, were similar to those estimated from the VSP signals using the kurtosis method. Thus, phase-only compensation with a combined scattering and intrinsic attenuation operator could work well depending on the seismic signal bandwidth and the distribution, depth, and magnitude of the impedance contrasts in the basalt sequence.