Since bottom water is just that and has not been exposed to the surface temps it will now react with sunlight and warmer or (different) temperatures in general. Higher Ortho P levels and nitrate levels will now get diluted also. But having those higher levels in the lower depths (nutrient sink) with out sunlight and cooler water may keep them from contributing to growth of FA & plankton and making themselves available for uptake by bottom rooted plants. Lower water PH levels may be raised and higher surface ph levels lowered. Other than natural mixing ponds become layered/ stratified. When aerating or circulating a body of water has to find a new "normal" and see what will thrive and struggle in this new eco system. Current anerobic bacteria will now be replaced with aerobic bacteria and as the pond bottom comes alive it will take some time for a pond "to find itself" and establish that new norm. This can take weeks or months as all ponds and lakes can react differently to aeration either bottom diffused or surface aeration.
