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Simulations hitherto performed with electron cyclotron resonance (ECR) ion sources (ECRIS) were mostly to predict physical quantities in their steady states. This article explores the time-dependent phenomena such as: interchange instability, ion production, and electron heating in order to simulate the time variations of hot-electron density, ion-trapping potential well, and core-electron temperature. This study has identified that the oscillations of around 1 Hz observable for these plasma parameters are a consequence of the interchange instability suffered by the hot electrons in the outer radial edge of an ECR shell. A pulsation of the ion-trapping potential well was found to take place under the unstable regime, thereby increasing the extractable ion current whenever the depth of the well is reduced due to the instability-triggered loss of electrons from the confinement. This finding may be exploited as a new method to obtain pulsed ion beams without pulsing the rf power. This article presents a formula for the best operating condition to achieve the highest steady ion beam currents out of an ECRIS. A self-consistent core-electron temperature was also predicted as a function of time. © 2000 American Institute of Physics.