Over the past several years, increasing attention has been directed towards understanding flow and contaminant transport processes occurring at the interface between surface water and groundwater, and a variety of modelling strategies have been proposed to couple these processes in a holistic, physically-based framework. Holistic management of watersheds and ecosystems requires such numerical models in order to forecast the impacts of activities such as land-use change, contaminant releases, or anthropogenic climate change, on water quantity and quality in both the surface and subsurface flow regimes. In this presentation, an overview of the capabilities and recent developments embedded in the HydroGeoSphere model will be presented together with several applications. HydroGeoSphere is an integrated 3D model designed to simulate water flow and advective-dispersive solute and heat transport on the 2D land surface and in the 3D subsurface under variably-saturated conditions. Full coupling of the surface and subsurface flow regimes is accomplished implicitly by simultaneously solving one system of non-linear discrete equations describing flow and transport in both flow regimes, as well as the water, solute and heat fluxes between continua. Other model features are the inclusion of heterogeneous material properties in all regimes, discrete fractures, dual-permeability flow and transport, canopy interception and evapotranspiration governed by plant and climatic conditions, as well as density-dependent flow and transport in the subsurface. The model capabilities and main features are demonstrated with several 3D numerical simulations performed for catchments of various scales. The examples range from the scale of an intensively-monitored rainfall-runoff-tracer experiment (~ 2000 m²), to a regional-scale watershed of about 300 km², to the continental scale that comprises a simulation of the impact of the Wisconsinian glaciation on groundwater flow system and groundwater age evolution (-120 k-year to present) over the entire Canadian land mass.