In tropical closed saline water aquaculture ponds, intermittent rainfall during the rainy season and strong solar radiation can cause salinity and thermal stratification, respectively. The combination of these stratifications may result in specific convection, known as thermohaline convection. Thermohaline convection is a type of double-diffusive convection that is observed in water bodies with two water densities. Thermohaline convection occurring in closed saline water ponds can induce heat storage in them. Heat storage in saline water aquaculture ponds is thought to be an important factor for controlling pond water quality, as the water environment can be affected by high water temperatures. Moreover, because heat storage is induced under the specific conditions of salinity stratification, salinity stratification also impacts physical water quality parameters. To clarify the relationship between heat storage and the variations in physical water quality associated with the formation of salinity stratification in saline water aquaculture ponds, continuous monitoring of weather and physical water quality parameters was conducted under culture conditions of fish and shrimp in Thailand. The results indicate the following: (1) Heat storage triggered by the rainfall-induced formation of salinity stratification can occur in shrimp culture ponds but is less likely to occur in fish culture pond; this is because the swimming behavior of fish can make formation of density stratification difficult. (2) When heat storage occurred in saline water aquaculture ponds, water temperature, turbidity, and dissolved oxygen were highly correlated in the heat storage layer, suggesting that high water temperature might affect microorganism activity in the ponds.