© 2016 Elsevier B.V. The GERDA experiment at LNGS of INFN is equipped with an active muon veto. The main part of the system is a water Cherenkov veto with 66 PMTs in the water tank surrounding the GERDA cryostat. The muon flux recorded by this veto shows a seasonal modulation. Two causes have been identified: (i) secondary muons from the CNGS neutrino beam (2.2%) and (ii) a temperature modulation of the atmosphere (1.4%). A mean cosmic muon rate of Iμ0=(3.477±0.002stat±0.067sys)×10−4/(s · m2) was found in good agreement with other experiments at LNGS. Combining the present result with those from previous experiments at LNGS the effective temperature coefficient αT,Lngsis determined to 0.93 ± 0.03. A fit of the temperature coefficients measured at various underground sites yields a kaon to pion ratio rK/πof 0.10 ± 0.03.