The physically-based integrated surface/subsurface water flow and solute/energy transport model, HydroGeoSphere, is designed to simulate 2D hydrological processes on the land surface together with 3D variably-saturated flow and transport in the subsurface. The model can explicitly account for the hydrologic, solute and thermal interactions between surface and subsurface flow regimes as well as the atmospheric inputs in terms of air temperature, solar radiation and sensible/latent heat fluxes. The applicability of the model has been demonstrated for a variety of problems, ranging from studies to improve the understanding of the physical and chemical processes in the water cycle of a small catchment to the assessment of the impact of climate change on water resources over the Canadian landmass in three dimensions. Downscaling issues involving hydrological simulations in a large basin or at the continental scale have been investigated to resolve the discrepancy in relevant scales for different physical processes.  A parallel computational framework has been implemented to facilitate model applications in high performance computing environments. Seamless integration of physicochemical processes and the enhancement and implementation of advanced numerical methods are essential to address many issues in water resource management such as the impact of climate change. Alterations of infiltration/exfiltration amounts across the land surface, baseflow to rivers due to changing subsurface flow patterns and fluctuations in the depth of the groundwater are examples of possible consequences of global climate change. To date, there are numerous studies concerning this issue in the literature, but many are limited to a relatively small domain, usually up to a watershed or basin scale, and/or they fail to simulate the surface and subsurface flow regimes in a physically-based, fully-integrated manner. As an application, the impact of long-term future climate change upon Canadian surface and subsurface water resources is examined in 3D using HydroGeoSphere after calibration against historical meteorological, hydrological and hydrogeological data.