Few studies of microbial biogeography address temporal variability in physicochemical conditions and communities in geothermal environments. Here we examine the temporal variability of 43 chemical analytes, temperature and pH in association with microbial community composition of 69 water samples collected bimonthly from 12 hotsprings of the Taupo Volcanic Zone between December 2015 and October 2016. Communities and physicochemical parameters were characterized using a combination of next generation Ion Torrent sequencing (16S rRNA), UV-spectrometry, ICP-MS, FIA and gas chromatography. Using correlation association tests, significant physicochemical changes (P<0.05) were correlated with temporal variations in microbial community composition in six of the target hotsprings. Of these six hotsprings, temperature and pH were the most influential variables associated with community changes and commonly covaried with the Aquificae, Deinococcus-Thermus and Proteobacteria at four sites. Downstream effects of rainfall using rainfall and geothermal bore water datasets could be linked with physicochemical and microbial community changes during the winter months at two of these sites. This study contributes to our understanding of geothermal microbial dynamics in stable and variable geothermal environme nts, and highlights that geothermal hotsprings are not isolated from their surrounding environment.