Abstract Cosmic ray induced neutrons and muons cause activation of nuclei. Using low-background detectors, constructed with strictly selected materials, and sufficient shielding from the surrounding environmental γ-radiation, one can measure the activation products and deduce information about the flux of neutrons and muons. The results of such a study can be used to improve the shielding for ultra-low counting spectrometry systems. In this work two low-level HPGe detection systems have been used to study the thermal and fast neutron fluxes, as well as the muon flux at three different experimental sites: on the surface, at a depth of 15 m water equivalent (m w.e.) and at 500 m w.e. The study was based on measuring the activation of nuclei in the detector itself and in gold foils. The muons were identified due to their high energy deposition in the detector crystal. Fast and thermal neutron fluxes have been measured since 1985 and estimates of the neutron and muon fluxes are given. The results are discussed and compared to the values obtained by the Kiel Neutron Monitor for the same time period.