I live in Middle Tennessee along the Highland Rim/Nashville Basin escarpment. Our pond dried up in May 2022 because the basin we used to capture a portion of the creek's water to pipe to the pond broke. (The creek dries up before reaching the pond due to a sinkhole.)

Dad and I are thinking about destroying the old pond dam and building a new, bigger one slightly further downstream reaching the same elevation before refilling it, turning the old pond into a small bay. (The pond existed before the family bought the land in the 1980s but had no permanent water until we worked on it in 2011.) We used sodium bentonite to make the tiny, deep pond hold the piped water, and we plan to do the same once we expand it into a very small lake. (The difference between the two is that lakes have an aphotic zone, and ponds don't.)

How should I go about making the refilled/expanded lake have places for shiner fish (maybe grass shrimp too) to hide from predatory fish (e.g. sunfish, bass, catfish)? I'd like for the shiners to be able to reproduce and feed the predatory fish constantly rather than just being an occasional treat introduced, replicating the natural environment. However, I'm not sure what to do. Here are a few ideas I've had so far.

1. I could strategically place rocks on the dry lakebed to give small animals a place to hide. However, I'm not sure how small the gaps would need to be to keep out medium fish like bluegill and pumpkinseed while still allowing small fish and freshwater shrimp to fit. I'm also not sure whether the rocks may leave a gap in the sodium bentonite we scatter that may compromise the ability of the lakebed to minimize seepage (especially given our karst topography). Last but not least, there's the fact that limestone gradually dissolves in water, chert is hard to break, and thin pieces of shale may be even more likely than limestone/chert cobbles to compromise the bentonite layer.
2. I thought of herbaceous aquatic vegetation, too. However, I'm not sure what species of herbaceous aquatic vegetation are native to the USA South/Midwest, and it'd need to be freshwater rather than brackish or saltwater. I wouldn't want to introduce anything that could become invasive or just die. Also, I'm not sure whether herbaceous vegetation would provide an adequate hiding place safe from bluegill, redeye, pumpkinseed, etc., given that it's relatively soft and flexible.
3. I thought of planting wetland trees/shrubs just below the maximum elevation that would be refilled before we refill it, too. However, I worry that, like rocks, that may compromise the bentonite layer too. I'm also not sure whether the bentonite may poison them, nor whether even bald cypresses and dwarf palmettos (let alone other native trees/shrubs) would be able to survive falling into water year-round and not just seasonally - to say nothing of my uncertainty as to whether bald cypresses tolerate juglone (which is an issue with the walnut trees in the vicinity). Last but not least, appearances of elevation can be deceptive, and the slightest mistake of a foot or even less could render the palmettos and cypresses still above water or too deep to survive (either of which would ruin our attempt).

Thanks in advance for any helpful advice!