I have a 1 acre pond connected to a 1/3 acre pond via an 18" culvert pipe.

I also have a ditch leading into the small pond to replenish the water level, that culvert utilizes a 15 inch diameter inflatable pipe plug from late Feb to early Nov to keep the pond water from draining out.

The watershed for these 2 ponds is not great, and I'm basically at the mercy of the seasonal rainfall when it comes to keeping the water level up. A typical year is 18" of water level loss from April-Sept. I have added a well, but it turned out to be only 4 GPM and I don't think that will help me much.

The attached picture shows where the culvert is (blue) and where the pipe plug is (red).

Pretty much all year round, when there isn't ice on the ponds, the larger pond is much clearer than the smaller pond. I have not made any tools to check clarity, but it's quite evident just by observation.

If on a given day I can see down 4 ft in the large pond, I'm lucky to see 1 ft down into the small pond.

I constructed both ponds in a similar fashion, with the same soils. I'm not sure what is going on.

Pond Clarity