Yep, you anticipated my next question - is your water level significantly lower during your hottest periods of the year? (By definition that is almost certainly statistically likely.)
Do you have a "saddle structure" in your pond? Do you aerate in the southern 12' deep bowl?
Your design with two separate deep bowls is NOT recommended in the typical state pond guidelines, BUT those guidelines typically are not set up for aeration and intensive management. Your design may inhibit natural aeration through wind action. Yet having one separate deep pool that is not mechanically aerated may result in your pond having an even lower average summer temperature.
(I can't remember Augie if you take DO measurements in your pond?)
