Nakhlite meteorites are igneous rocks from Mars that were aqueously altered ~630 million years ago. Hydrothermal systems on Earth are known to provide microhabitats; knowledge of the extent and duration of these systems is crucial to establish whether they could sustain life elsewhere in the Solar System. Here, we explore the three-dimensional distribution of hydrous phases within the Miller Range 03346 nakhlite meteorite using nondestructive neutron and x-ray tomography to determine whether alteration is interconnected and pervasive. The results reveal discrete clusters of hydrous phases within and surrounding olivine grains, with limited interconnectivity between clusters. This implies that the fluid was localized and originated from the melting of local subsurface ice following an impact event. Consequently, the duration of the hydrous alteration was likely short, meaning that the martian crust sampled by the nakhlites could not have provided habitable environments that could harbor any life on Mars during the Amazonian.