Fluid flow in the upper crust not only impacts the redistribution of heat and elements, driving the formation of economic ore deposits, but it also exerts control on metamorphism, metasomatism, and deformation. However, reconstructing the history of fluid flow in ancient basins is exceedingly difficult, particularly in Archean sedimentary rocks because of extensive overprinting and recrystallization. Here, we report U-Pb ages for monazite and xenotime that grew in bedding-parallel veins in 2.63–2.5-b.y.-old shales along the southern Pilbara craton, Australia. The U-Pb ages define six discrete populations, at 2.41 Ga, 2.30 Ga, 2.20 Ga, 2.10 Ga, 2.05 Ga, and 1.66 Ga, which formed ≥200 m.y. after deposition. The abundance of bedding-parallel crack-seal and fibrous veins in banded iron formations (BIFs) and underlying shales suggests a history of episodic buildup of fluid pressure followed by microfracturing, fluid expulsion, and mineral growth. Thermometry of vein minerals indicates temperatures between 230 °C and 320 °C, implicating the migration of hydrothermal fluids. The development of bedding-parallel veins at 2.41 Ga, 2.20 Ga, and 1.66 Ga was coeval with regional orogenic events known to have affected the craton, whereas vein growth at 2.30 Ga, 2.10 Ga, and 2.05 Ga reveals new episodes of deformation and fluid flow. Our results show that well-preserved Archean shales devoid of structural fabrics and >150 km inboard of the craton margin preserve a cryptic history of fluid overpressure, crack-seal vein development, and hydrothermal fluid flow between 2.41 and 1.66 b.y. ago.