Isotopic analysis of precipitation over the Andaman Island, Bay of Bengal was carried out for the year 2012 and 2013 in order to study the atmospheric controls on rainwater isotopic variations. The oxygen and hydrogen isotopic compositions are typical of the tropical marine sites but show significant variations depending on the ocean-atmosphere conditions; maximum depletion was observed during the tropical cyclones. The isotopic composition of rainwater seems to be controlled by the dynamical nature of the moisture rather than the individual rain events. Precipitation isotopes undergo systematic depletions in response to the organized convection occurring over a large area and are modulated by the integrated effect of convective activities. Precipitation isotopes appear to be linked with the monsoon intraseasonal variability in addition to synoptic scale fluctuations. During the early to mid monsoon the amount effect arose primarily due to rain re-evaporation but in the later phase it was driven by moisture convergence rather than evaporation. Amount effect had distinct characteristics in these two years, which appeared to be modulated by the intraseasonal variability of monsoon. It is shown that the variable nature of amount effect limits our ability to reconstruct the past-monsoon rainfall variability on annual to sub-annual time scale.