Assessment of rainfall, fluctuations in water table and variations in the radon data of multi-parametric geophysical observatory (MPGO), Ghuttu is performed during the Kedarnath event, June 16–17, 2013. During this extreme event, continuous rainfall for 52 h caused huge loss of life and property. This kind of continuous and intensive rainfall is the first and only single occasion during the period of past more than 17 years since the setup of MPGO. The rapid rise in the water table due to continuous rainfall is a distinctive event and anomalous changes are also noticed in other geophysical time series. The high variations are seen in the radon concentration at the observation site. By applying statistical procedures it is found that the radon counts are crossing the limit of twice of standard deviation from the average value during the flash flood period. The effects in soil radon and water radon are found to be opposite during the extreme rainfall period. To identify the seasonal variability in radon time series we performed power spectrum technique analysis. We found the presence of 6–10 days periodicities in the radon time series with significant amplitudes. The spectrogram of both radon and water level variation time series indicate changes at the same time suggesting hydrological changes in radon emanation. It implies a distinctive result for the earthquake precursory research of MPGO for treating seismic and non-seismic anomalous changes in radon.