The ionosphere is variable in space and time. Some of the changes are chemical in origin and can be readily understood on the basis of the general considerations outlined above. There is a systematic variation, for example, according to the time of day. In early morning the Sun is relatively low in the sky, so that radiation must penetrate a large column of air before reaching a given level of the atmosphere. As a result, ionization rates are lower, and the location of ionized layers shifts to higher altitudes. As the Sun rises, the D, E, and F₁ layers shift in altitude. The layers are lowest and densities of electrons are highest at noon. At night, on the other hand, ionization in the D, E, and F₁ regions tends to disappear as electrons and ions recombine to form neutral gases.

The diurnal, or daily, variation of the F₂ layer is less dramatic. Ions produced at high altitudes during the day maintain a sizable density of electrons at the F₂ peak throughout the day and then diffuse downward at night. This accounts for the fact that radio reception (both in the broadcast and shortwave bands) is generally best at night. Ionization at lower altitudes—primarily those corresponding to the D region—tends to interfere with radio transmissions during the day. Interference is minimal at night because ionization in the D layer effectively disappears with the setting of the Sun.

The density of ionization varies in response to changes in the intensity and properties of radiation from the Sun. The output of solar energy is relatively constant in the visible and near-ultraviolet portions of the spectrum. It varies appreciably, however, at shorter wavelengths, reflecting changes in the temperature of the outermost regions of the solar atmosphere. The changes are particularly large, in excess of a factor of 10, at X-ray wavelengths. Variations in the D region are correspondingly large, with smaller though still significant changes in the E and F layers.

Solar activity varies on a characteristic timescale of about 11 years. It is not entirely periodic, however; successive cycles can differ significantly, and there are indications that activity can be low for centuries. The Sun was quiet for more than 200 years from about 1600 to about 1850. Solar activity was particularly intense in 1958.

As noted in the section on Mechanisms of ionization, ionization above the F₂ peak is removed mainly by downward diffusion of ions and electrons. Ions are constrained, however, to move along the magnetic field. The field is oriented horizontally at the magnetic equator, which is equidistant between the magnetic North Pole and the magnetic South Pole, so vertical diffusion is inhibited at low latitudes. The density of ionized atomic oxygen (O⁺) and electrons at low latitudes is therefore controlled by chemistry to a larger extent than at high latitudes. The F₂ peak is correspondingly higher in altitude, and the density of electrons is elevated accordingly.

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Ions and electrons formed at high altitudes and low latitudes are transported to higher latitudes by thermospheric winds. As a result, the highest density of electrons at the F₂ peak is observed at intermediate latitudes, offset from the magnetic equator by about 10 degrees.

Transport can also affect the distribution of ionization at lower altitudes. The diurnal pattern of heating in the troposphere and stratosphere excites a spectrum of waves, some of which are free to propagate vertically. The amplitude of the waves grows significantly as the disturbance enters regions of lower density. Passage of the waves is associated with strong alternating horizontal winds. Ionization can be driven up inclined magnetic field lines at one altitude, while winds blowing in an opposite direction at higher altitudes can induce simultaneous downward motion. This can lead to a bunching of ionization—a local enhancement of the electron density. The mechanism is particularly important in the E region and is responsible for the phenomenon known as sporadic E.

The buildup of ionization is normally limited by dissociative recombination of molecular ions. At D and E region altitudes, however, the ionosphere contains a small but variable concentration of atomic ions, derived from ionization of metals ablated from meteorites. The density of metallic ions—notably those of sodium (Na⁺), magnesium (Mg⁺⁺), and potassium (K⁺)—is sometimes high enough to supply a layer of ionization with a density comparable to that of the F layer. This can result in a major temporary disruption of radio communications.

Winds generated in the lower ionosphere by thermal forcing from below have characteristic periods expressed as submultiples of a day. Waves with a period of 24 hours dominate at low latitudes, whereas those with a characteristic period of 12 hours are more important at high latitudes. The origin of the waves is basically similar to that of oceanic tides caused by the pull of lunar gravity. The vertical motion that generates ionospheric waves, however, is the result of the diurnal pattern of heating and cooling rather than gravity. Additional waves can arise owing to irregular forcing, associated, for example, with thunderstorms, motion over mountain ranges, and other small-scale meteorological disturbances. These small-scale disturbances are referred to as gravity waves to distinguish them from the more regular planetary-scale motions excited by the diurnal cycle of heating and cooling. The regular response to thermal forcing is known as the atmospheric tide.

Tides and gravity waves have similar effects on ionization in the E region. They both are responsible for concentrating ionization in layers. In combination with the large-scale system of winds in the lower thermosphere, they are also effective in driving an irregular current that flows in the E and lower F regions of the ionosphere. The current owes its origin to differences in the facility with which motions of ions and electrons are constrained by the magnetic field. It is associated with an electric field and results in a modulation of the magnetic field that can be readily detected at the surface. The current is particularly intense in the equatorial region, where it is known as the electrojet. The region of strong current flow is known as the dynamo region.

Protons (H⁺) and helium ions (He⁺) are important components of the ionosphere above the F₂ peak. They increase in abundance relative to ionized atomic oxygen (O⁺) with increasing altitude. Protons are produced by photoionization of atomic hydrogen (H), hv + H → H⁺ + e (9) and by charge transfer from O⁺ to H, O⁺ + H → O + H⁺. (10) Helium ions are formed by photoionization of helium. The distribution of H⁺ and He⁺ with altitude reflects the influence of the polarization electric field set up to preserve charge neutrality. When O⁺ is the dominant ion, the polarization field acts to lift H⁺ and He⁺ with a force equivalent, but in opposite direction, to that exerted by the gravitational field on a particle with a mass of eight atomic units, as described in the section on Diffusion. Protons behave as though they have an effective gravitational mass of −7 atomic units (−7 = 1 − 8). The effective mass of He⁺ is −4 atomic units (−4 = 4 − 8).

The abundance of H⁺ and He⁺ increases with altitude. Eventually H⁺ becomes the dominant component of the outermost ionosphere, which is sometimes referred to as the protonosphere. The more uniform composition of the atmosphere at this level causes a reduction in the polarization field to one equivalent to the gravitational force acting on a body with a mass of 0.5 atomic unit, directed upward for ions and downward for electrons. This field is sufficient to maintain equal densities of H⁺ and electrons. The effective masses of O⁺ and He⁺ shift to 15.5 atomic units (15.5 = 16 − 0.5) and 3.5 atomic units (3.5 = 4 − 0.5), respectively, and the abundance of O⁺, He⁺, and H⁺ declines with further increases in altitude.