Two troughs in Noctis Labyrinthus display a diversity of mineral assemblages rarely seen spatially collocated on Mars. Minerals identified from Mars Reconnaissance Orbiter data within the troughs include polyhydrated and monohydrated sulfates, an Al clay (e.g., kaolinite or beidellite), Fe/Mg smectites, hydrated silica and/or opal, and a leached clay or jarosite mixture with a doublet absorption between 2.2 and 2.3 μm. Units both pre-date and post-date smaller pits and depressions within the larger troughs, indicating that deposition was coeval with continued extension, collapse, and erosion in the Late Hesperian to Early Amazonian (2–3 Ga). The strata within each trough display a mineralogic diversity consistent with active aqueous processes and/or changing chemical conditions over time, perhaps due to hydrothermal alteration of volcanic ash, influxes of groundwater from nearby Tharsis volcanism, fumarole activity, and melting snow and/or ice. The superposition of younger Fe/Mg smectites over sulfates, Al clays, and hydrated silica and/or opal in both troughs indicates that this region is unique relative to most other locations on Mars, where the opposite progression is observed and the Fe/Mg smectites are Noachian (older than 3.6 Ga) in age. Consequently, these troughs may have been habitable regions on Mars at a time when drier conditions dominated the surface.