We coupled the process-based National Integrated Catchment-based Eco-hydrology (NICE) model to an urban canopy model and the Regional Atmospheric Modeling System to simulate the effect of urban geometry and anthropogenic exhaustion on the hydrothermal changes in the atmosphere/land and the interfacial areas of the Japanese megalopolis. The simulation was conducted with multiscale in horizontally regional-urban-point levels and in vertically atmosphere–surface–unsaturated–saturated layers. The model reasonably reproduced the observed hydrothermal values by using ground-truth data in various types of natural/artificial land covers. The simulated results also suggested that the latent heat flux in the new water-holding pavement (consisting of porous asphalt and water-holding filler made of steel by-products based on silica compound) has a strong effect on hydrologic cycle and cooling temperature in comparison with the observed heat budget by newly incorporating the effect of water amount on the heat conductivity in the pavement. Furthermore, the model predicted the hydrothermal changes under two types of land cover scenarios to promote evaporation and to reduce air temperature against heat island phenomenon. Finally, we evaluated the relationship between the effect of groundwater use to ameliorate the heat island and the effect of infiltration on the water cycle in the catchment. These procedures to integrate the multiscaled model simulation with political scenario based on the effective management of water resources as heat sink/source would be very powerful approaches for recovering a sound hydrologic cycle and for creating thermally pleasing environments in the megalopolis. Copyright © 2012 John Wiley & Sons, Ltd.