what about adding a dam into the narrow connection between the 2 ponds ---that way you can use one as a control pond for lack of a better word I can think of ---then use the smaller of the 2 ponds as your fish pond in a very large aquaponics farm -----do a bunch of floating pools for lettuces and some flood and drains and some towers ---heck the possibilities are endless when ya have that much of a water source

my thinking on why to separate the 2 ponds is 2-fold ---they could leave the one side as a somewhat natural setting for animals ----plus if the farm-pond gets too outta whack of a ph ya can pump some from the natural pond to it --or vice versa