The spatial and temporal dynamics of the North Sea ecosystem are dependent upon vertical mixing processes which modify the availability of light and limit nutrients for phytoplankton production. In order to examine the effects of inter and intra annual variations in stratification on ecosystem dynamics we have developed and tested a potential energy model of thermal stratification based on the energy equation (for turbulence). The energy equation relates the temporal and spatial changes of turbulent kinetic energy (TKE), the production of TKE and the dissipation of TKE to the change of potential energy as water masses of different densities are mixed in the field of gravity. A constant ratio between the gain in potential energy and the production of TKE is assumed, known as the flux Richardson number. The model is comprised of 0·5m vertical layers with a temporal time step of 1 day. The model is forced with wind, dew point temperature from Ekofisk oilfield in the central North Sea, and tidal current and atmospheric radiation. The model is used to simulate the seasonal cycle of stratification in the central North Sea in the years 1988, 1989 and 1990 and is compared to density profiles in these years available from the ICES hydrographic database. We find that the model is able to simulate variations in thermal stratification including the seasonal onset and breakdown of stratification, the thermocline depth, and the effects of discrete wind and cooling events. For the years 1988–1990 we find an R2=0·97 between observed and predicted upper layer temperatures. However, the model is less successful in the prediction of temperatures of the intermediate and deep layers (R2=0·46 and 0·14) due to small deviations in thermocline depth and variations in tidal amplitude. The model was then applied to examine potential differences in stratification between the years 1990 and 1996. Simulations suggested that the development of stratification is very rapid in 1990 and that the spring of 1996 is very cold. Both of these observations having the potential to impact on the efficiency of lower trophic level coupling and production.