The Copper Flat hydrothermal system in Hillsboro, New Mexico, USA, is hosted by a partially brecciated porphyritic quartz monzonite intrusive body. Igneous rocks are alkaline to calc-alkaline, and chondrite-normalized rare earth element (REE) plots show enrichment in REEs that is consistent with other regional Laramide igneous rocks. Five assemblages of weak to moderate intensity phyllic alteration with distinct paragenetic relationships exist at the deposit and are classified as: early phyllic, quartz-sericite-pyrite (QSP), sericite-quartz, sericite-carbonate and late QSP. Carbonate is common and is part of some phyllic and the potassic alteration assemblages. Carbonates and phyllosilicates were analyzed by electron microprobe. White micas show substantial substitution of Al by Fe and Mg, and secondary biotite is Mg-rich. Relative to other porphyry Cu systems, the micas from Copper Flat contain, on average, greater F. Carbonates from veins and the replacement of mafic silicates and feldspars were determined to be mostly calcite, but reduced metal carbonates such as ankerite and rhodochrosite are also present in the alteration assemblages. The fluid(s) responsible for alteration are inferred to be CO2-rich and pH neutral as interpreted from the widespread presence of carbonates in both the potassic and phyllic alteration zones, and the white mica composition. Carbonate mineral compositions and absence of sulfates in the potassic alteration suggest that the hydrothermal fluids were not highly oxidized and were sulfur-poor. These features of alteration and geochemistry at Copper Flat are atypical of most porphyry Cu-Mo deposits in the southwestern U.S. and may be more characteristic of porphyry Cu-Au and porphyry Mo deposits.