I won't get into the management thing since I don't know anything about managing moist soil for waterfowl. But, I know how the lakes work so I want to say a few things...

The physical parameters and limitations of the system (ignoring local rain, evaporation, etc)

A) All the inflows into the Santee Cooper lakes system (Marion and Moultrie) come into Marion through the Congree/Saluda and Wateree rivers (the highest inflows I know of were around 140,000 cfs),
B) There are three ways for these inflows to get out of Marion 1) The Diversion Canal, 2) The Marion hydro (tiny only about 600cfs), and 3) Spilling through the Marion Dam
C) The only way significant inflows get into Lake Moultrie are through the Diversion Canal,
D) The only ways to get water out of Moultrie are through Jefferies Hydro (28,000 cfs max) and St. Stephen Hydro (24,500 cfs max),
E) The maximum through the Diversion Canal is about 30,000 cfs so Jefferies and St. Stephens can't be run at maximum for any length of time,
F) The only way to get water through the Diversion Canal is to have a differential between the elevations of Lakes Marion and Moultrie. Moultrie has to be about 2 feet lower than Marion in order to get 25,000 cfs flowing through the Diversion Canal (this is why Moultrie is so much lower than Marion during times of heavy inflows),
G) Water down the Santee = 1) Marion Hydro + 2) Spilling at Marion Dam + 3) St. Stephen Hydro + 4) local rain into the Santee watershed below Lake Marion,
H) Water down the Cooper = 1) Jefferies Hydro - Note: the Cooper River watershed is very small below Jefferies so there is very little flow from local rain below Moultrie.

Operational parameters:

1) It's the Corp. of Engineers that limits the water that Santee Cooper (the utility) can send water down the Cooper, not the FERC (to reduce the amount of dredging in Charleston Harbor),
2) By contract, Jefferies Hydro must average 4,500 cfs +/- 5% every week - the only exception is during times of drought when the Corp. of Engineers will allow a lower amount of water to be run through Jefferies,
3) Jefferies Hydro is never allowed by the Corp. of Engineers to exceed the 4,500 cfs average,
4) Santee Cooper can't, nor should they able to, run both St. Stephen (about 24,500 cfs max) and Jefferies hydros (about 28,000 cfs max) at the their maximum since the Diversion Canal was only designed for about 30,000 cfs.

So, what can be done to reduce the big water events in the area between Winyah and Cape Romain?
During significant spilling (say >10,000 cfs), St. Stephens should be limited to <3,000 cfs and Jefferies Hydro run at or near its maximum - this will shave 20,000 cfs of the top of every flood event in the lower Santee.

As I mentioned in G4 - there is significant additional inflows into the lower Santee during coastal rain events. I suspect, but don't know for sure, that development in these coastal areas has made this worse, maybe much worse. I know how to fix that but people won't like it...haha