Abstract This paper mainly reviews our recent work on the biology and geochemistry of foraminifera with respect to their use as palaeoceanographic proxies. Our approach to proxy validation and development is described, primarily from a modeler's point of view. The approach is based on complementary steps in understanding the inorganic chemistry, inorganic isotope fractionation, and biological controls that determine palaeo-tracer signals in organisms used in climate reconstructions. Integration of laboratory experiments, field and culture studies, theoretical considerations and numerical modelling holds the key to the method's success. We describe effects of life-processes in foraminifera on stable carbon, oxygen, and boron isotopes as well as Mg incorporation into foraminiferal calcite shells. Stable boron isotopes will be used to illustrate our approach. We show that a mechanism-based understanding is often required before primary climate signals can be extracted from the geologic record because the signals can be heavily overprinted by secondary, non-climate related phenomena. Moreover, for some of the proxies, fundamental knowledge on the thermodynamic, inorganic basis is still lacking. One example is stable boron isotopes, a palaeo- p H proxy, for which the boron isotope fractionation between the dissolved boron compounds in seawater was not precisely known until recently. Attempts to overcome such hurdles are described and implications of our work for palaeoceanographic reconstructions are discussed.