The New Afton deposit is hosted within the Cherry Creek member of the Iron Mask batholith complex, a multi-phase plutonic body exposed in a southeast-trending belt measuring 34 kilometers long by 5 kilometers wide. At New Afton, the Cherry Creek intrusive is a variably and multiply-brecciated assemblage of porphyritic and equigranular monzonite and monzodiorite. Structure is a dominant feature of the geology of the deposit and has influenced all aspects of the host rock lithology, mineralizing events, and post-ore processes. East-northeast-striking steeply-dipping fault zones were the primary control to the New Afton mineralization. Two faults, termed the Hanging Wall (east) and Foot Wall (west) constrain the New Afton deposit to a relatively narrow northwest-southeast-striking near-vertical corridor.

The New Afton deposits are copper-gold silica-saturated, alkalic porphyry style deposits. The primary mineralizing event was preceded by development of disseminated magnetite-pyrite. Primary economic sulphide mineralization occurred in association with potassic alteration (principally K-spar) resulting in the destruction of the earlier magnetite-pyrite assemblage. Following this, carbonate veinlets (principally ankerite) developed along and surrounding the faults along with varying amounts of pyrite, clay gouge and sericite. Weathering processes have altered the primary sulphide mineralization, imposing an irregular zonation of mineral species.

Primary hypogene sulphide mineralization occurs as disseminated and fracture-filling chalcopyrite and bornite. The exterior boundary of this zone is defined as the first appearance of copper sulphide accompanied by disappearance of magnetite-pyrite. The deposit has been subject to weathering and oxidation processes but this weathering is unconventional in distribution. There is no oxide cap over top of the primary sulphide mineralization. Instead, fractures have conducted weathering fluids downwards in a relatively confined area but to significant depths (>500 m in places). Mesogene (or mixed) zone mineralization is defined by the first appearance of chalcocite. The chalcocite can occur as total replacements of, or rims surrounding chalcopyrite and bornite. The appearance of native copper defines the boundary of the supergene zone.