Perdido Cove RV Resort over on the Florida side (Pensacola) is on the waterway. It has boat docks for your water based yacht as well as spots for the land based one. There is also another, Playa Del Rio, that is just across on the Florida side on Perdido Beach Blvd. Playa Del Rio is a bit tight. I don't know of any in Gulf Shores right on the inter-coastal waterway. Bay Breeze on the Bay, Ft Morgan Rd, Gulf Shores, is directly on Bon Secour Bay. They have a small beach and nice pier/dock. Myself, I don't know that I would want eat anything caught there in the inter-coastal.
Travel well, travel safe,
2006 Tiffin Phaeton - 2011 Cadillac SRX