Although the depth of the water just off the land that is directly on the bay is generally too shallow for a marina, the bayous off the bay are often deeper and some could be used for a marina of sorts, as long as there is a deep enough channel between the bayou and the bay. There are a few of the new developments in Freeport that are building a marina as part of the plan. I think there is at least one being built on LaGrange Bayou. I don't think it's a public marina though. LaGrange is a nice wide deep bayou and there is a ship builder on this bayou that takes advantage of this fact.
Many of the marinas (Okaloosa, Shalimar) have been slowly closing due to being bought out by condo developers. I have a friend that has been looking for a place to dock his boat in the area and currently has it in Niceville, but would love to have it in Freeport. However, I don't think there are many areas in Walton County that are currently zoned for this type of activity.