Abstract Radon and thoron exhalation rates from samples are estimated by the standard closed-loop technique using online radon monitors. Conventionally, the mass balance equation is formulated by considering the closed air volume of the sample chamber and the detector chamber put together. This model serves the purpose of estimating the radon/thoron exhalation rates for the prescribed pump flow rate of 1 L min−1 using RAD7 online monitor. The flow rate requirement is crucial for thoron measurement due to its short half-life. In the present work, an alternate model is proposed which simulates the dynamics of radon/thoron concentration dictated by the air entry and exit rate and brings out the effect of pump flow rate. This model is more of academic interest, where sample chamber and detector chamber are considered as two separate entities since they are separated by tubing. The mass balance equation is reformulated considering the air entry and exit in and out the individual chambers. The radon buildup in the sample chamber and detector chamber were treated separately by two coupled differential equations. The equations were numerically solved. The model reiterated the fact that the lower flow rates do not affect the buildup profile of relatively long-lived 222Rn (half-life 3.8 d) and its steady-state concentration attained in the closed air volume. However, experiments carried out for flow rates 0.3 and 0.5 L min−1 with RAD7 monitor using powdered granite sample with higher 226Ra and 232Th concentrations gave contradicting results. The radon effective removal rate was found to decrease with increase in flow rate from 0.3 to 1 L min−1. This issue was investigated, and it was speculated that the thoron interference problem might not be properly addressed for flow rates <1 L min−1. This was ascertained by observing the effective radon removal rate in the absence of thoron by conducting radon decay experiments with different flow rates. For the case of short-lived thoron (half-life 55 s), the model described the dynamics of thoron concentration in the closed loop and the steady-state concentrations attained in the detector and sample chamber. As expected, the model showed that due to decay losses during transit of thoron between the chambers, the steady-state concentrations attained in the chambers considerably differ from each other even for 1 L min−1 flow rate.