While September pretty much marks the end of "tourist season", kayaking season really never ends in Southeast North Carolina.
September and October lead to cooler temperatures, which means instead of 90's in the afternoon, it's in the 80's, or even the 70's
"Fall" is apparent in the marsh as the grasses become a different shade of green, and the shorter length of the days leads to less planktonic algae and the water starts to become crystal clear.
High pressure, blue sky days are common through November, and make for a great day out on the water.
If the wind does kick up and a windy marsh paddle isn't your thing, this is a great time to check out one of the local lakes or streams. Greenfield Lake, tucked into downtown Wilmington, is a haven for wading birds, turtles, and gators. (They don't attack kayaks! If you see them in the winter they will be basking to get whatever solar warmth they can get. You are not on the menu). The entirety of Greenfield Lake can be leisurely paddled in about 2 hours, and you'll most likely forget that you are in the middle of town.
If you're up for a paddling adventure, and don't mind putting on some layers to keep you nice and warm, getting out on the water is a year-round event in Wilmington.