A Radio Telescope is a very sensitive radio receiver with as large directional antenna attached. The signals received from outer space are very weak and although radio signals pass through the atmosphere with minimum affect there are other factors in the upper atmosphere that can interfere with these signals.
Ionospheric Effects
The ionosphere is a region in the upper atmosphere that extends from about 70 to 500 km in altitude. In this region atoms can have their outer electrons removed by extreme ultra-violet (EUV) and X-ray radiation coming from our sun. Consequently, the atmosphere here is partially ionized, hence the name ionosphere. An ionised gas (or plasma) is conductive and so will interact with electromagnetic signals (radio waves) that pass through it.
At lower frequencies (below 30Mhz) a plasma will increasingly attenuate or reflect radio signals and it is this property that allows shortwave signals to circle the globe. However for the Radio Astronomer this is barrier to extraterrestrial signals and it is the reason why most radio astronomy is conducted above ~18Mhz. At higher frequencies, although the signal will not be reflected it but may still be refracted or attenuated.
Also as the ionosphere is not uniform the density changes with the time of day (diurnal), along with season variations and is highly affected by solar activity. Consequently it will contain irregularities such as patches, clumps, and troughs of ionisation and cause numerous effects to the signal passing through.
Scintillation
Scintillation, which is similar to the visible twinkling of stars in the night sky, is caused by small-scale irregularities in the ionosphere. So instead of a uniform layer of ionisation the ionosphere will be subject to patches of lower or higher density ionisation. These irregularities preferentially form in two different regions over the Earth - the Polar (both north and south), and the equatorial regions.
In the Polar Regions ionospheric irregularities are caused by particles precipitating down into the ionosphere from the magnetosphere and are the same particles that produce the visible aurora theses flows of particles cause bubbles and troughs and are not stable.
Auroral scintillations may occur at any time of day, but tend to be stronger at night, and when geomagnetic activity is high. In the equatorial regions, after sunset, bubbles of ionisation form at the bottom of the ionosphere and rise upward during the night forming vertical plumes. Signals that propagate near the edges of these plumes are subject to the most intense scintillations.
Equatorial scintillations are thus basically a night-time phenomenon, with most of the plumes disappearing by midnight, although some do persist into the early morning hours. Equatorial scintillations increase in strength as the sun's extreme ultra-violet (EUV) and X-ray output increases which produce thicker and more strongly ionised ionosphere. Their intensity follows the approximately 11 year solar cycle. They also display a 27 day periodicity due to the solar rotation.
Faraday Rotation
When a plane a polarised radio signal travels through a the ionosphere, in which a magnetic field such as the Earth's the plane of polarisation is rotated. The amount of rotation is proportional to the magnitude of the magnetic field and the total ionisation through which the signal passes.
Low frequencies suffer greater rotation than high frequencies as the ionosphere becomes more ionised due to increasing solar flux and so signals traversing the ionosphere at low elevation angles will be affected more than signals propagating near the zenith.
At VHF frequencies and high solar activity levels, the plane of polarisation may be rotated through many times 360 degrees. Although most natural radio sources have random polarisation this does add additional signal interference.
Tropospheric Absorption and other Effects
Tropospheric weather conditions, "conventional" weather occurring in the lower 10 km of the atmosphere, can also cause losses in signals propagating to the ground. Water vapour is particularly damaging to signals above about 2 GHz, causing absorption of signals which becomes greater as the frequency increases. 10-20 GHz is particularly susceptible, and precipitation causing total loss of signal.
At frequencies above 20 GHz we start to encounter resonant absorption at specific frequencies. Oxygen, in particular, will absorb electromagnetic energy only at certain well-defined frequencies. These frequencies correspond exactly to the energies required to lift the Oxygen atoms into higher energy states and so Radio Astronomers also avoid these frequency bands.