Shallow water mass characteristics such as temperature and density profile play a critical role in the climate system. We have developed a new method by which to reconstruct the ancient shallow water mass stability on the continental shelf using oxygen isotope variation within mollusc shells and fish otoliths and applied the method to an important interval in Earth history, the most recent transition from Greenhouse (Eocene) to Icehouse (Oligocene) climate modes. We define the slope of summer temperature (density) versus the seasonal range in temperature (density) as an indicator of water mass stability. In addition, extrapolation of the regression to zero seasonality is a proxy for temperature at the bottom of the seasonal thermocline (TBST). During the greenhouse world (the early Eocene and middle Eocene) the water mass plot shows an unstable water mass, agreeing with previous planktonic foraminiferal studies showing that temperature gradients at this time were much smaller than at present. During the middle to late Eocene transition, a substantial increase in water mass stability occurred. Significant cooling (~5¿C) of the TBST at this transition indicates that the greater cooling of deeper water relative to surface water caused the increase in water mass stability. The changes in water column structure at this transition were the most likely cause of a major extinction of planktonic foraminifera from warm to cold water taxa. The late Eocene T-ΔT profile is very similar to modern profiles, suggesting that shallow water mass structure became similar to that of the modern Gulf Coastal shelf by the late Eocene. At the Eocene/Oligocene (E/O) boundary, no major change in water mass structure is identified. This agrees with the observation that no major extinction of planktonic foraminifera is found at the E/O boundary.