The essential state of the Phanerozoic ocean-atmosphere system with respect to major lithophile and organic components can be bounded by sedimentary observational data and relatively few model assumptions. The model assumptions are in turn sufficient to constrain and compute the remaining fluxes that result in a comprehensive model describing atmospheric and oceanic evolutionary history over the past 500 m.y. that is in accord with the sedimentary observational data. Two central themes emerge. First, there is a strong coupling of the state of various reservoirs throughout the entire system imposed mainly by negative physical, chemical and biological feedbacks. Second, there is a significant overprint of ‘physical’ processes, such as weathering, by biologically-mediated processes and ecosystem evolution. Ultimately, the Phanerozoic is characterized by two modes of seawater major-ion chemistry, pH and carbonate saturation state, and atmospheric CO2. Importantly, the transition between these two modes may result from the previous state of the system whose impacts lag by tens of millions of years. Thus, the instantaneous state of the system at any given point in time may reflect in part the ‘memory’ of a previous period when fluxes and processes were not in balance. The modern-day problem of ocean acidification mainly reflects the fact that human activities of fossil fuel burning and land use changes are resulting in geologically rapid releases of CO2 to the atmosphere and its absorption by the surface ocean and does not reflect the longer term processes and feedbacks that led to the acidic oceans of the past.