A higher drought risk in Java Island is generally known than the other regions in Indonesia. Tracking soil moisture can be an alternative way to monitor drought rather than precipitation-based drought indices. The objective of this study was to assess root-zone water storage (defined by root-zone soil moisture contents) based on a linked approach between the generalized complementary relationship (GCR) and a single bucket model in Java Island. Since it does not require precipitation for estimating actual evapotranspiration (ETa), the GCR allowed implementation of a simple single bucket model. The ETa and root-zone soil moisture estimated in this study were compared against the Global Land Evaporation Amsterdam Model (GLEAM) and the root-zone water storage additionally compared with the European Centre for Medium-Range Weather Forecasts (ECMWF) ERA5 reanalysis data products. Overall, the GCR ETa estimates were higher than those from GLEAM, and similar patterns of the root-zone water storage were found in the comparisons of both GLEAM and ERA5. The comparative evaluation suggests a further study on the adjustment of Priestley-Taylor coefficient value in Java for better application of the GCR. The soil moisture estimated by the single bucket model and the root-zone soil moisture products of GLEAM were highly correlated (0.8 or greater Pearson correlation coefficients). Low root-zone water storage and high ETa rates were found in eastern Java relative to the other areas, indicating high water shortage risks in dry season. This study found that El Niño clearly contributed to the variability of the root-zone water storage in Java especially in wet seasons (December to February). It is also suggested that the proposed approach can be useful to operationally provide soil water availability in Java from readily available meteorological observations.