This dataset contains information about the stable oxygen and hydrogen isotope composition (δ18O, δ2H and d-excess) of waters within the Five Lakes of Mikata catchment. Datapoints span March 2011 – January 2012 and July 2020 – July 2022. Samples include precipitation on an event-basis, weekly river water and weekly lake water. To accompany the precipitation isotope composition data, total precipitation and average temperature during each subsampling period is provided. Water temperature and salinity variations with depth within Lake Suigetsu on six dates across the 2020 – 2022 sampling interval are also given. This data was collected to determine if catchment water composition reflects East Asian Monsoon variability. This work was supported by an Australian Research Council Discovery Project (DP200101768), a JSPS KAKENHI Grant (19K20442) and the NERC IAPETUS2 Doctoral Training Partnership.