Geochemical data from cap carbonates deposited above Cryogenian glacial deposits have been widely used to infer the conditions that prevailed in the aftermath of snowball Earth. However, the time scale over which these carbonates were deposited and the degree to which they record the chemistry of a globally well-mixed ocean have remained poorly constrained. During deglaciation, a large volume of meltwater entered the ocean, creating two distinct layers: the fresh, hot, and light upper layer, and the salty, cold, and dense lower layer. Here we estimate the ocean mixing time scale based on energetic constraints. We find that the mixing time scale is 104–105 yr, with a best estimate of ∼5 × 104 yr, or up to 100 times longer than that of the modern ocean. Mixing of the surface temperature anomaly implies a delayed sea-level rise of 40–50 m associated with pure thermal expansion. This result reconciles geological, geochemical, and paleomagnetic data from basal Ediacaran cap carbonates with physical oceanographic theory. In particular, our model suggests that (1) the cap dolostones formed predominantly in a freshwater environment; (2) the waters in which the dolostones formed were not well mixed with saline deep water, allowing for large geochemical differences between the cap dolostones and the deep ocean; and (3) the cap carbonate sequences formed in a two-phase transgression that lasted >104 yr, which is consistent with both local sea-level records and the preservation of magnetic excursions and reversals.