Subsurface fluid flow and heat transport play an important role in many geological processes, such as hydrocarbon migration, structural geology, plate tectonics, diagenesis, and metamorphism (Ingebritsen and Sanford, 1999), and in particular they have major implications for both the formation and preservation of almost every class of economic ore deposit, especially those in sedimentary basins. This chapter is dedicated to addressing fundamental theory and numerical modeling technique of fluid flow and heat transport in subsurface porous media as well as presenting two application examples associated with ore genesis under different geological conditions. The chapter is organized into four sections. The first section is aimed at theoretical aspect of fluid flow and heat transport. It first introduces major physical processes involved in a hydrothermal flow system and outlines a variety of driving mechanisms deemed responsible for large-scale groundwater flow (i.e., topography, buoyancy, tectonic deformation, and sediment compaction), and then describes the mathematical equations that govern and control the behavior of subsurface fluid migration and thermal regime. It ends up with deriving an analytical solution using the Laplace transformation to address the heat transport process subject to a constant fluid flow in a single fracture embedded in an impermeable host porous medium. The second section concentrates on the numerical modeling aspect of fluid flow and heat transport by detailing the Galerkin finite element technique that is capable of numerically simulating complex hydrothermal flow systems. Noticing that topography and buoyancy are the two top driving forces commonly encountered in reality and that the interactions between them are still poorly understood, the third section is therefore attempts to quantify the relative importance of these two mechanisms in driving fluid transport via a series of numerical experiments, and also to determine under what conditions both topography- and buoyancy-driven flows coexist and under what conditions one flow system dominates the other. The fourth section of this chapter focuses on the application aspect of fluid flow and heat transport associated with the formation of mineral deposits, including the Sedex-type lead-zinc deposits in northern Australia (with buoyancy as the primary driving force), and the Dachang polymetallic deposits in southern China (with tectonic deformation as the primary driving force).