Plasma inhomogeneities extending along geomagnetic field lines in the ionosphere and magnetosphere can have a vortex structure. Electromagnetic waves can propagate in plasma inhomogeneities in the waveguide channel mode. It has been indicated that energy and particle fluxes related to the development of small-scale electrostatic turbulence in a magnetized plasma with an unstable electron component promotes an increase in plasma density gradients in the walls of waveguide channels and an enhancement in plasma vortices. At low L shells in the region of the geomagnetic equator, the development of plasma electrostatic instability and the damping of drifting plasma vortices in the inhomogeneous geomagnetic field in the topside ionosphere can be the main mechanism by which large-scale (∼1000 km) regions with a decreased plasma density are formed.