Abstract The radon (222Rn) and thoron (220Rn) fluxes from the soil and building materials are the major contributors to their indoor levels. Hence, the measurement of radon and thoron exhalation rates from the source matrix becomes the foremost step in controlling the indoor radon and thoron exposure. It is a challenge to measure the exhalation rates without disturbing the natural conditions. The back-diffusion phenomenon modifies the exhalation rate. The work presented here is to measure the back-diffusion coefficient and takes it into consideration while estimating the exhalation rate. For radon measurements, the back-diffusion coefficient and the free exhalation rates were simultaneously estimated by adopting a novel methodology. The leak rate of the experimental setup measured by this methodology was agreeable with the value measured by adopting the standard technique. In the case of thoron, the back-diffusion effect was found to be negligible for the present experimental conditions and it is duly explained. The above results were obtained by analyzing two soil samples with high 238U and 232Th content collected from monazite-rich coastal area.