The integrative and comprehensive analysis considering the spatial and temporal representation of the hydrological process, such as the distribution of rainfall, land cover and land use, is a challenge for the water resources management. In tropical areas, energy availability throughout the year defines the rainfall distribution and evapotranspiration rate according to vegetation heterogeneity. To quantify water balance in tropical areas including these heterogeneities in the soil-vegetation-atmosphere relationship, we developed a fully distributed hydrological model called the Rainfall Runoff Balance Enhanced Model (RUBEM). The model was developed under a physics-based process structure, using remote sensing data to represent soil-water balance patterns, such as evapotranspiration, interception, baseflow, lateral flow, recharge, and runoff. The calibration procedure was based on nine global parameters. RUBEM could represent the spatio-temporal heterogeneities (soil, land use and land cover (LULC), topography, vegetation, and climate) in three basins in a tropical area. The results showed good adherence between the processes governing the soil-vegetation-atmosphere relationship according to the humidity indicator and the runoff coefficient. Overall, RUBEM can be used to help improve the management and planning of integrated water resources under climate, land use, and land cover changes in tropical regions.