This paper presents an investigation on the effects of superimposed temperature deviations as a control technique for the flows and mixing in lower half heated upper half cooled enclosures. Results show that the strength of the wall layer depends on the difference between the wall surface temperature and the fluid core temperature. The location of the head-on collision between a pair of upward/downward wall layers, which controls the mixing and fluid exchange between the two halves, is determined by the wall layer flow momentum strengths. Elevating/reducing the wall temperature by a superimposed temperature deviation is an effective control for the flow and mixing in such enclosures. Heat transfer analysis shows that the superimposed temperature deviations have minor effects on the total heat flow rate from the lower walls. Thus, this technique can be applied onto reactor vessels without modifying the reactor vessel configuration.