To calibrate δ18O time-series from speleothems in the eastern Indian summer monsoon (ISM) region of India, and to understand the moisture regime over the northern Bay of Bengal (BoB) we analyze the δ18O and δD of rainwater, collected in 2007 and 2008 near Cherrapunji, India. δD values range from + 18.5‰ to − 144.4‰, while δ18O varies between + 0.8‰ and − 18.8‰. The Local Meteoric Water Line (LMWL) is found to be indistinguishable from the Global Meteoric Water Line (GMWL). Late ISM (September–October) rainfall exhibits lowest δ18O and δD values, with little relationship to the local precipitation amount. There is a trend to lighter isotope values over the course of the ISM, but it does not correlate with the patterns of temperature and rainfall amount. δ18O and δD time-series have to be interpreted with caution in terms of the ‘amount effect’ in this subtropical region. We find that the temporal trend in δ18O reflects increasing transport distance during the ISM, isotopic changes in the northern BoB surface waters during late ISM, and vapor re-equilibration with rain droplets. Using an isotope box model for surface ocean waters, we quantify the potential influence of river runoff on the isotopic composition of the seasonal freshwater plume in the northern BoB. Temporal variations in this source can contribute up to 25% of the observed changes in stable isotopes of precipitation in NE India. To delineate other moisture sources, we use backward trajectory computations and find a strong correlation between source region and isotopic composition. Palaeoclimatic stable isotope time-series from northeast Indian speleothems likely reflect changes in moisture source and transport pathway, as well as the isotopic composition of the BoB surface water, all of which in turn reflect ISM strength. Stalagmite records from the region can therefore be interpreted as integrated measures of the ISM strength.