Thermal performance of passive residual heat removal systems and solar heaters is affected by thermal stratification in the pool. There are hardly any studies reported in the literature on the role of seismic excitations on thermal stratification in water pools. This work focuses on the experimental investigation of thermal stratification in a pool under the seismic condition with the horizontally mounted heater simulating the heat exchanger. Effects of heater submergence depth, frequency of excitation, and amplitude of displacement on the thermal stratification have been investigated experimentally. It was observed that the heater submergence depth has significant effect on thermal stratification in the pool. When the water pool is subjected to an external excitation, the pool water separates into two zones; convective and impulsive. If the heater is in the impulsive zone, excitation effects are not found. If heater is close to convective zone, significant effects on thermal stratification are observed. However, it is observed that only first mode of excitation with large amplitude helps to achieve complete thermal mixing. Higher modes of excitation have the minimal effect on thermal stratification mitigation. Nondimensional stratification number has been evaluated to explain the mitigation of thermal stratification with seismic excitation.