The biogeochemical cycling of major and minor elements in the ocean has direct bearing on the health of the planet and its inhabitants. Reactive intermediates, of both chemical and biological origin, are emerging as important players in these biogeochemical cycles. Due to their rapid production and consumption, these reactive intermediates are short-lived and typically in low concentration. Involvement of these “invisible” species in biogeochemistry may therefore be hidden, or cryptic, with no obvious lingering chemical signature. Here, we highlight reactive intermediates of the oxygen, manganese, and sulfur cycles and how these intermediates are involved in cryptic cross-linkages between marine biogeochemical cycles of global importance.