Swarm electron density (Ne) observations from the Langmuir probe (LP) can detect ionospheric disturbances at the altitude of a satellite. Along-track satellite observations provide a large number of very short observations of different places in the ionosphere, where Ne is disturbed. Moreover, different perturbations occupy various Ne signal frequencies. Therefore, such short signals are more recognizable in two dimensions, where aside from their change in time, we can observe their diversity in the frequency domain. Spectral analysis is an essential tool applied here, as it enables signal decomposition and the recognition of composite patterns of Ne disturbances that occupy different frequencies. This study shows a high-resolution application of short-term Fourier transform (STFT) to Swarm Ne observations in the Papua New Guinea region in the vicinity of earthquakes, tsunamis, and related general seismic activity. The system of tectonic plate junctions, including the Pacific–Australian boundary, is located orthogonally to Swarm track footprints. The selected wavelengths of seismically induced ionospheric disturbances detected via Swarm are compared with the three sets of three-month records of seismic activity: in the winter solstice of 2016/2017, when seismic activity was highest, and in the summer solstice and vernal equinox of 2016, which were calmer. Moreover, more Swarm data records are analyzed at the same latitudes for validation purposes, in a place where there are no tectonic plate boundaries that are orthogonal to the Swarm orbital footprint. Additional validation is supplied through Swarm Ne observations from completely different latitudes, where the Swarm orbital footprint orthogonally crosses a different subducting plate boundary. Aside from the seismic energy, the solar radio flux (F10.7), equatorial plasma bubbles (EPBs), and geomagnetic ap and Dst indices are also reviewed here. Their influence on the ionospheric Ne is also found in Swarm observations. Finally, the Pearson correlation coefficient (PCC), applied to the pairs of 3-month time series created from Swarm Ne variations, seismic energy, ap, Dst, and F10.7, summarizes the graphical inspection of mutual correlations. It points to the predominant correlation of Swarm Ne disturbances with seismicity, especially during nighttime. We show that most of the Ne disturbances at a selected wavelength of 300 km correlate more with seismicity than with geomagnetic and solar indices. Therefore, Swarm LP can be assessed as being capable of observing the lithosphere–atmosphere–ionosphere coupling (LAIC) from the orbit.