We present observations from the Falkland Islands Super Dual Auroral Radar Network radar of the propagation of HF radio waves via the Weddell Sea Ionospheric Anomaly (WSA), a region of enhanced austral summer nighttime ionospheric electron densities covering the southern Pacific and South Americas region. This anomaly is thought to be produced by uplift of the ionosphere by prevailing equatorward thermospheric winds. Of particular interest are perturbations of the WSA-supported propagation, which suggest that during periods of geomagnetic disturbance, the ionospheric layer can be lowered by several tens of kilometers and subsequently recover over a period of 1 to 2 h. Perturbations can appear singly or as a train of two to three events. We discuss possible causes of the perturbations and conclude that they are associated with equatorward propagating large-scale atmospheric waves produced by magnetospheric energy deposition in the auroral or subauroral ionosphere. Changes in high/middle latitude electrodynamics during geomagnetic storms may also account for the perturbations, but further modeling is required to fully understand their cause.