One of the best natural experiences in the area is north of Charleston at Cape Romain National Wildlife Refuge (5801 Hwy. 17 N., 843/928-3264, www.fws.gov/caperomain [1], sunrise–sunset year-round). Essentially comprising four barrier islands, the 66,000-acre refuge—almost all of which is marsh—provides a lot of great paddling opportunities, chief among them Bull Island (no overnight camping).
A fairly lengthy trek from where you put in lies famous Boneyard Beach, where hundreds of downed trees lie on the sand, bleached by sun and salt. Slightly to the south within the refuge, Capers Island Heritage Preserve (843/953-9300, www.dnr.sc.gov [2], daily dawn–dusk, free) is still a popular camping locale, despite heavy damage from Hurricane Hugo.
Get permits in advance by calling the South Carolina Department of Natural Resources. You can kayak to the refuge yourself or take the only approved ferry service from Coastal Expeditions (654 Serotina Ct., 843/881-4582, www.coastalexpeditions.com [3]).
Barrier Island Eco Tours (50 41st Ave., 843/886-5000, www.nature-tours.com [4]) on Isle of Palms [5] also runs trips to the area.
Links:
[1] http://www.fws.gov/caperomain
[2] http://www.dnr.sc.gov
[3] http://www.coastalexpeditions.com
[4] http://www.nature-tours.com
[5] http://www.moon.com/destinations/charleston-savannah/charleston/sights/east-cooper/isle-palms