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Zinc (Zn) is a key micronutrient for marine phytoplankton, with a global distribution that is similar to silicic acid. The processes that govern this relationship, despite the very different biological cycling of Zn and silica, remain poorly understood. Here, we use diagnostic and mechanistic models to show that only a combination of Southern Ocean biological uptake and reversible scavenging of Zn onto sinking particles can explain the observations. The distinction between organic and adsorbed Zn can also reconcile the vertical distribution and mass balance of Zn isotopes, which previously appeared at odds. This holistic understanding explains the Zn deficiencies observed throughout the low-latitude ocean and implies a greater sensitivity of the marine Zn cycle to climate-driven changes in organic matter cycling than previously recognized.