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 effects have been identified which are caused by secondary muons from the CNGS neutrino beam (2.2 %) and a temperature modulation of the atmosphere (1.4 %). A mean cosmic muon rate of $I^0_{mu} = (3.477 pm 0.002_{textrm{stat}} pm 0.067_{textrm{sys}}) times 10^{-4}$/(s$cdot$m$^2$) was found in good agreement with other experiments at LNGS at a depth of 3500~meter water equivalent.
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