Despite high costs and lengthy deployments, satellite communications have traditionally been used to provide coverage in remote areas. However, given the fact that there is no radio infrastructure available in these areas, Near Vertical Incidence Skywave (NVIS) technology has positioned itself as an attractive alternative to communicate with low-power nodes in remote areas. This type of communication works in the HF frequency range complying with STANAG and MIL-STD standards, which define a physical layer for scenarios that differ from NVIS and low-power communication. The purpose of this paper was to present the definition of a new communication physical layer based on single-carrier frequency-domain equalization (SC-FDE) based on these standards but adapted to the ionospheric communication channel. This physical layer was compared to an OFDM-based layer from a previous study. The experiments performed show that this new approach achieves better results than OFDM in terms of a higher signal quality with a higher specific BER probability. Finally, this layer was also used in the theoretical design of an NVIS gateway to link sensor network devices spanning large-scale remote areas in a secure manner in the context of ubiquitous sensor networks (USN).