27 pages, 8 figures, review paper, submitted to Astroparticle PhysicsAstroparticle physics and cosmology allow us to scan the universe through multiple messengers. It is the combination of these probes that improves our understanding of the universe, both in its composition and its dynamics. Unlike other areas in science, research in astroparticle physics has a real originality in detection techniques, in infrastructure locations, and in the observed physical phenomenon that is not created directly by humans. It is these features that make the minimisation of statistical and systematic errors a perpetual challenge. In all these projects, the environment is turned into a detector medium or a target. The atmosphere is probably the environment component the most common in astroparticle physics and requires a continuous monitoring of its properties to minimise as much as possible the systematic uncertainties associated. This paper introduces the different atmospheric effects to take into account in astroparticle physics measurements and provides a non-exhaustive list of techniques and instruments to monitor the different elements composing the atmosphere. A discussion on the close link between astroparticle physics and Earth sciences ends this paper