Step 1: Understanding the Concept:
Deep water bodies in warm seasons develop vertical density and temperature stratification dividing the water column into distinct horizontal zones.
Step 2: Detailed Explanation:
Thermal stratification in lakes and deep storage ponds establishes three distinct thermal layers:
1. Epilimnion: The uppermost, sun-warmed, low-density, well-mixed, and oxygen-rich surface layer.
2. Thermocline (Metalimnion): The middle transition zone exhibiting a rapid drop in water temperature with increasing depth ($> 1^\circ\text{C}$ per meter).
3. Hypolimnion: The deep, bottom-most, dense, dark, and coldest layer of water that remains unmixed and often experiences dissolved oxygen depletion.
Step 3: Final Answer:
Thus, the layer of cooler water is the Hypolimnion, matching option (A).