Unusual decimeter-scale structures occur in the sediment-hosted Black Butte Copper Mine Project deposit within lower Mesoproterozoic strata of the Belt Supergroup, Montana. These low domal and stratiform lenses are made up of millimeter-scale, hollow or mineral-filled tubes bounded by pyrite walls. X-ray micro–computed tomography (micro-CT) shows that the tube structures are similar to the porous fabric of modern diffuse hydrothermal vents, and they do not resemble textures associated with the mineralization of known microbial communities. We determined the sulfur isotopic composition of sulfide minerals with in situ secondary ion mass spectrometry (SIMS) and of texture-specific sulfate phases with multicollector–inductively coupled plasma–mass spectrometry (MC-ICP-MS). The sedimentological setting, ore paragenesis, sulfur isotope systematics, and porosity structure of these porous precipitates constrain the site of their formation to above the sediment-water interface where metalliferous hydrothermal fluids vented into the overlying water column. These data constrain the geochemistry of the Mesoproterozoic sediment-water interface and the site of deposition for copper-cobalt-silver mineralization. Metals in the hydrothermal fluids titrated sulfide in seawater to create tortuous fluid-flow conduits. Pyrite that precipitated at the vent sites exhibits large sulfur isotope fractionation (>50‰), which indicates a close association between the vents and sulfate-reducing microbiota. In the subsurface, base metal sulfides precipitated from sulfide formed during the reduction of early diagenetic barite, also ultimately derived from seawater. This model suggests dynamic bottom-water redox conditions at the vent site driven by the interplay between sulfate-reducing organisms and metalliferous fluid effluence.