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Abstract The modulation of low-energy galactic cosmic rays reflects interplanetary magnetic field variations and can provide useful information on solar activity. An array of ground-surface detectors can reveal the secondary particles, which originate from the interaction of cosmic rays with the atmosphere. In this work, we present an investigation of the low-threshold rate (scaler) time series recorded in 16 yr of operation by the Pierre Auger Observatory surface detectors in Malargüe, Argentina. Through an advanced spectral analysis, we detected highly statistically significant variations in the time series with periods ranging from the decadal to the daily scale. We investigate their origin, revealing a direct connection with solar variability. Thanks to their intrinsic very low noise level, the Auger scalers allow a thorough and detailed investigation of the galactic cosmic-ray flux variations in the heliosphere at different timescales and can, therefore, be considered a new proxy of solar variability.