Pelican Rest is a great marina, although not well located. Galveston Yacht Basin is in a much better location, but the marina is not in great repair.
Clear Lake has several good live aboard marinas. Seabrook Shipyard is well located, but security isn't great. Watergate, Portofino, and Waterford are good marinas and well located. South Shore is a nice marina with hotel attached, but it's a long way to the Bay and in a north wind the water gets very shallow. Blue Dolphin can be OK, but some of the slips are shallow.
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