The Permian records one of the most extreme climate transitions of the Phanerozoic, yet the climatic and environmental dynamics of this interval and their effects on neritic carbonate systems remain poorly constrained. New stratigraphic and carbon isotope records from uppermost Pennsylvanian to Lower Permian strata of the Orogrande Basin in south-central New Mexico, USA, provide fresh insights into the response of palaeotropical carbonate systems to the growth and demise of ice sheets on Gondwana. The earliest Permian acme of glaciation is recorded in the Orogrande Basin as a series of subaerial exposure surfaces marked by highly variable δ13C values that tend toward values as low as −6‰. These stratigraphic and isotopic patterns are interpreted to reflect the retreat of the sea from the basin during glacial expansion. Younger (Lower Sakmarian to Kungurian) strata, deposited during the long decline of the Late Paleozoic Ice Age, are characterized overall by higher and more uniform δ13C values (+2 to +5‰) and show no evidence of long-term subaerial exposure. However, these strata record two short-lived excursions toward more negative δ13C values. These excursions occur through intervals that record shifts toward shallower and more restricted conditions in the Orogrande Basin. The timing of these shifts corresponds to two periods of glacial expansion across eastern Australia during Late Sakmarian to Early Artinskian and Kungurian time. These relationships suggest that pulses of glacial expansion in eastern Gondwana were of sufficient magnitude to have caused relative sea-level fall, and possibly environmental change, in the Orogrande Basin. The results from this study suggest that marine chemistry, depositional environments and sea-level in the Orogrande Basin were profoundly influenced by epochs of Gondwanan glaciation. These inferences help improve the understanding of how palaeotropical carbonate systems responded to the effects of cryospheric changes during the acme and waning stages of the Late Palaeozoic Ice Age.