Hydrothermal systems hosted by submarine arc volcanoes commonly include a large component of magmatic fluid. The high Cu-Au contents and strongly acidic fluids in these systems are similar to those that formed in the shallow parts of some porphyry copper and epithermal gold deposits mined today on land. Two main types of hydrothermal systems occur along the submarine portion of the Kermadec arc (offshore New Zealand): magmatically influenced and seawater-dominated systems. Brothers volcano hosts both types. Here, we report results from a series of drill holes cored by the International Ocean Discovery Program into these two types of hydrothermal systems. We show that the extent of hydrothermal alteration of the host dacitic volcaniclastics and lavas reflects primary lithological porosity and contrasting spatial and temporal contributions of magmatic fluid, hydrothermal fluid, and seawater. We present a two-step model that links the changes in hydrothermal fluid regime to the evolution of the volcano caldera. Initial hydrothermal activity, prior to caldera formation, was dominated by magmatic gases and hypersaline brines. The former mixed with seawater as they ascended toward the seafloor, and the latter remained sequestered in the subsurface. Following caldera collapse, seawater infiltrated the volcano through fault-controlled permeability, interacted with wall rock and the segregated brines, and transported associated metals toward the seafloor and formed Cu-Zn-Au–rich chimneys on the caldera walls and rim, a process continuing to the present day. This two-step process may be common in submarine arc caldera volcanoes that host volcanogenic massive sulfide deposits, and it is particularly efficient at focusing mineralization at, or near, the seafloor.