Estuarine freshwater transport has a substantial impact on the near-shore ecosystem and coastal ocean environment away from the estuary. This paper introduces two independent methods to track the Mekong freshwater-induced mass transport by calculating the time lag (or equivalently, the phase) between in situ Mekong basin runoff and the equivalent water height (EWH) time series over the western South China Sea from a gravity recovery and climate experiment (GRACE). The first method is the harmonic analysis that determines the phase difference between annual components of the two time series (called the P-method), and the other is the cross-correlation analysis that directly obtains the time lag by shifting the lagged time series forward to attain the highest cross-correlation between the two time series (called the C-method). Using a three-year rolling window, the time lag variations in three versions of GRACE between 2005 and 2012 are computed for demonstrating the consistency of the results. We found that the time lag derived from the P-method is, on average, slightly larger and more variable than that from the C-method. A comparison of our gridded time lag against the age determined via radium isotopes in September, 2007 by Chen et al. (2010) revealed that our gridded time lag results were in good agreement with most isotope-derived ages, with the largest difference less than 6 days. Among the three versions of the GRACE time series, CSR Release 05 performed the best. The lowest standard deviation of time lag was ~1.6 days, calculated by the C-method, whereas the mean difference for all the time lags from the isotope-derived ages is ~1 day by P-method. This study demonstrates the potential of monitoring Mekong estuarine freshwater transport over the western South China Sea by GRACE.