Large magnitude (>10‰) carbon-isotope (δ13C) excursions recorded in carbonate-bearing sediments are increasingly used to monitor environmental change and constrain the chronology of the critical interval in the Neoproterozoic stratigraphic record that is timed with the first appearance and radiation of metazoan life. The ~10‰ Bitter Springs Anomaly preserved in Tonian-aged (1000–720 Ma) carbonate rocks in the Amadeus Basin of central Australia has been offered as one of the best preserved examples of a primary marine δ13C excursion because it is regionally reproducible and δ13C values covary in organic and carbonate carbon arguing against diagenetic exchange. However, here we show that δ13C values defining the excursion coincide with abrupt lithofacies changes between regularly cyclic grainstone and microbial carbonates, and desiccated red bed mudstones with interbedded evaporite and dolomite deposits, recording local environmental shifts from restricted marine conditions to alkaline lacustrine and playa settings that preserve negative (−4‰) and positive (+6‰) δ13C values, respectively. The stratigraphic δ13C pattern in both organic and carbonate carbon recurs within the basin in a similar way to associated sedimentary facies, reflecting the linkage of local paleoenvironmental conditions and δ13C values. These local excursions may be time transgressive or record a relative sea-level influence manifest through exposure of sub-basins isolated by sea-level fall below shallow sills, but are independent of secular seawater variation. As the shallow intracratonic setting of the Bitter Springs Formation is typical of other Neoproterozoic carbonate successions used to construct the present δ13C seawater record, it identifies the potential for local influences on δ13C excursions that are neither diagenetic nor representative of the global exogenic cycle.