A minimum value in the Dissolved Oxygen distribution of two shallow lakes namely, Rabindra Sarobar in south Kolkata and Subhas Sarobar in East Kolkata in the Gangetic Delta plain, has been observed to develop in the Hypolimnion during the stratified period. This minimum is usually explained by the accumulation of organic matter from the overlying layer of water. The introduction of organic matter from allochthonous and autochthonous sources is also a likely contributor to the accelerated oxygen depletion within Hypolimnion. The thermal stratification, in general, which occurs in these tropical lakes, is of direct relevance in maintaining the water quality standards, particularly for higher aquatic life. The present article attempts to investigate the possible depletion of hypolimnetic oxygen depletion as a result of the impact of thermal stratification.  These investigations will be the basic guidelines for the fishermen and their livelihoods potentially depend upon the different varieties of fishing on daily basis. The massive summer fish kills in these lakes is a major devastating happenings that is reported by the fishermen and also it is well evident from our experimental observations.  The comparison of the biodiversity of these two lakes is attempted in the present investigation. Key Words: Thermal stratification, Dissolved Oxygen, Tropical Shallow Lake, Hypolimnion, biodiversity