Otoliths, the biomineralized stones in the inner ear of fish, grow continually throughout the whole of an individual’s life – from embryo to death. Functionally, otoliths play a role in maintaining balance and proper hearing. As they are largely metabolically inert, they can be treated as a “black box”, recording the specifics of the physico-chemical environment experienced by a fish at any given point in its life. As a result, they are routinely used to reconstruct both growth and environmental histories. Currently, the biomolecular mechanisms that underpin otolith formation, growth and composition are largely unknown, as fewer than a dozen otolith proteins have been described. To address this shortcoming, we created a tissue-specific transcriptome for the inner ear and brain of a southern Australian fish, black bream (Acanthopagrus butcheri), which was used to identify proteins in proteomic data for otoliths and endolymph (inner ear fluid) from adult fish. We identified more than 350 proteins present in the otolith, revealing the potential mechanisms for how otolith nucleation occurs, the controls on daily increment deposition, the likely metal incorporation sites in the organic matrix, and the evidence, at the biochemical level, for their metabolic stability.