Traditional theories for the structure of the main thermocline exclude any effects of mesoscale eddies. We investigate the effects of such eddies on the thermocline by integrating an eddy resolving wind and buoyancy forced primitive equation ocean model in simple box and channel configurations. In the absence of eddies and in the low diffusivity limit, the depth of the upper, advectively dominated thermocline scales as the Ekman pumping strength to the half power, and the thickness of the diffusive thermocline at the base scales as the diffusivity to the half power. Using an equilibrated low resolution simulation as the initial conditions, an eddying simulation is run to near thermal equilibrium. In general, the eddying case still displays the signature of the `two-thermocline' limit, with advective dynamics dominating in the upper thermocline and an explicitly diffusive region at the base. However, the isothermal mode water of the low resolution run is partially mixed away by eddies as they seek to reduce the overall potential energy of the flow. Although the internal structure of the thermocline is altered by eddies, the depth of the thermocline changes only modestly, except close to the western boundary current. In the central part of the gyre, the eddy terms do not participate in the dominant balance of the temperature equation in the upper ventilated thermocline and thus do not change the scaling for the thermocline depth.

Near the surface, the eddies have diabatic effects that cannot be parameterized by advection terms; however, away from the surface our results are consistent with the notion that eddies are mixing thickness (or potential vorticity) along isopycnals, but they mix inefficiently across isopycnals. The eddies do typically enter into the dominant balance of terms at the thermocline base. However, because the abyssal water has different properties to that of the ventilated thermocline and because eddy effects are predominantly adiabatic, explicit diapycnal diffusion remains an important term in the thermodynamic equation, although its effect on mixing water masses is small.