Deep mineral exploration is increasingly important for finding new mineral resources but there are many uncertainties. Understanding the factors controlling the localization of mineralization at depth can reduce the risk in deep mineral exploration. One of the relatively poorly constrained but important factors is the hydrodynamics of mineralization. This paper reviews the principles of hydrodynamics of mineralization, especially the nature of relationships between mineralization and structures, and their applications to various types of mineralization systems in the context of hydrodynamic linkage between shallow and deep parts of the systems. Three categories of mineralization systems were examined, i.e., magmatic-hydrothermal systems, structurally controlled hydrothermal systems with uncertain fluid sources, and hydrothermal systems associated with sedimentary basins. The implications for deep mineral exploration, including potentials for new mineral resources at depth, favorable locations for mineralization, as well as uncertainties, are discussed.