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Particulate inorganic carbon (calcium carbonate mineral) is produced by pelagic calcifying organisms in the upper layers of the open ocean, it sinks to the deep sea, is partly dissolved and partly stored in the geological archive. This phenomenon, known as the carbonate pump, is an important component of the global carbon cycle and exerts a major influence on climate. The amount of carbonate mineral produced depends on the evolutionary and ecological success of calcifying pelagic organisms. The formulation of adequate predictive carbonate pump modules raises the problem that the behaviour of this highly diverse set of organisms needs to be taken into account. To overcome this difficulty, we propose a “model system” approach, whereby a single representative organism, the coccolithophore Emiliania huxleyi , is investigated in detailed interactive experimental and modelling studies. To construct a comprehensive model of the carbonate pump, subsequent research is envisaged on additional representative organisms, but this work is likely to be facilitated by the experience gained with E. huxleyi . The model system approach permits (1) an emphasis on the non-linear character of the fluxes; (2) a focus on the coupling of the carbonate pump with other climatically important phenomena — the organic carbon pump and DMS production; and (3) exploitation of the experimental accessibility of the E. huxleyi system.