The Cherenkov Telescope Array (CTA) is the future ground-based observatory for gamma-ray
astronomy at very high energies. The atmosphere is an integral part of every Cherenkov telescope.
Different atmospheric conditions, such as clouds, can reduce the fraction of Cherenkov photons
produced in air showers that reach ground-based telescopes, which may affect the performance.
Decreased sensitivity of the telescopes may lead to misconstructed energies and spectra. This study
presents the impact of various atmospheric conditions on CTA performance. The atmospheric
transmission in a cloudy atmosphere in the wavelength range from 203 nm to 1000 nm was
simulated for different cloud bases and different optical depths using the MODerate resolution
atmospheric TRANsmission (MODTRAN) code. MODTRAN output files were used as inputs
for generic Monte Carlo simulations. The analysis was performed using the MAGIC Analysis
and Reconstruction Software (MARS) adapted for CTA. As expected, the effects of clouds are
most evident at low energies, near the energy threshold. Even in the presence of dense clouds,
high-energy gamma rays may still trigger the telescopes if the first interaction occurs lower in the
atmosphere, below the cloud base. A method to analyze very high-energy data obtained in the
presence of clouds is presented. The systematic uncertainties of the method are evaluated. These
studies help to gain more precise knowledge about the CTA response to cloudy conditions and
give insights on how to proceed with data obtained in such conditions. This may prove crucial for
alert-based observations and time-critical studies of transient phenomena.