Current cap carbonate formation models invoke a number of different alkalinity sources for the Neoproterozoic deglacial ocean (e.g., weathering alkalinity, hydrothermal alkalinity, microbial sulfate reduction (MSR) alkalinity, and methane oxidation alkalinity). Assessment of the competing models depends in part on an evaluation of their proposed alkalinity source(s). In the Nanhua rift basin of South China, recently discovered Sturtian cap carbonates on horsts have the potential to address this issue owing to sedimentological and geochemical differences between them and correlative deepwater deposits from adjacent grabens. Cap carbonates at three sites in northeastern Guizhou Province, China were selected for petrographic, XRD, XRF, ICP-MS, in-situ LA-ICP-MS, and Sr and Nd isotope analyses to evaluate the conditions and processes under which they formed: (1) JJS, a high-energy shallow-water (platform) setting that accumulated white laminated dolostone and pisolitic grainstone, (2) ZK01, an intermediate-depth (upper slope) setting that accumulated dark-gray laminated dolostone, and (3) ZK4207, a deep-water (basinal) setting that accumulated organic-rich Mn‑carbonates of the basal Datangpo Formation. The salinity proxy B/Ga records brackish conditions at JJS (4.7 ± 1.2) versus fully marine conditions at ZK01 (7.5 ± 0.8) and ZK4207 (9.1 ± 2.0). Hydrothermal influences, as proxied by high Eu/Eu*, trace-metal (Co, Ni, Cu, V) enrichments, and radiogenic SrNd isotopic compositions, were strong in the latter sections but absent at JJS. These observations document the existence in the post-Sturtian Nanhua Basin of a reduced-salinity surface layer presumably containing a large glacial meltwater component and lacking hydrothermal inputs, and a fully marine deep watermass subject to strong hydrothermal inputs. Carbonate δ13C variation between JJS (−2 to +2‰), ZK01 (−4 to 0‰), and ZK4207 (−7 to −6‰) records a pronounced vertical carbon-isotope gradient in the Nanhua Basin, consistent with elevated marine productivity in the context of strong salinity/density stratification. Massive inputs of alkalinity from meltwater sources are supported by a ∼ 3.5× greater flux to surface-layer dolomitic cap carbonates than to basinal Mn‑carbonates during the Sturtian deglaciation, although strong correlations between intermediate/deep-water carbonates and hydrothermal proxies imply that basin-floor vents were an additional source of alkalinity. Our study provides insight into the mechanisms of formation of cap carbonates generally, with implications for both Sturtian and Marinoan cap carbonate deposits on other cratons.