The difficulty of achieving a seal with compacted clay is strongly affected by hydrostatic pressure. If you are impounding water by the creek that is only 3 feet deep, then you don't have much hydrostatic pressure that is constantly trying to push through your clay.

Do you get down to a good clay layer at depth within the basin of your ponds by the creek? If so, there is a chance you could doze/excavate clay out of that spot and put a blanket seal on your berm, and not worry about the rocks in the core of the berm. For a 3 foot deep pond, there is a good chance that a single 6 inch lift of clay that is well compacted would seal the pond.

Of course, the thinner you go, the higher likelihood that animals digging, plant roots digging, etc. will eventually work their way through your clay blanket. If you have the equipment out to do 6 inches of clay blanket, then you could probably do one or even two more lifts for not that much additional cost - especially if you have the clay material nearby.

P.S. If you are letting your duck ponds go dry for part of the year, then you do NOT want 100% clay for your seals. Pure clay will dehydrate and shrink during extended dry periods and cause cracks in your berm seals. I think silty, sandy clay with about 30-35% clay content would probably hold up best for your application. Just make sure it is well mixed during the transportation and spreading process. (However, that specific advice about optimal clay content is outside of my area of expertise. You might check Mike Otto's book to see if he addresses that problem.)