There are several marinas at Port Isabel.
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The causeway crossing the Intracoastal Waterway between Port Isabel and Padre Island has a fixed span with a clearance of 73 feet.
Just north of Port Isabel, a dredged channel branches off the Intracoastal Waterway in a SW direction towards the Port Isabel small-boat basin. The channel turns S before entering the basin and, once inside, turns SE to a turning basin. In 2010, the controlling depths were 2.6 feet in the entrance channel, thence 3 feet in the harbor channel and in the basin.
Port Isabel, about 2.5 miles W from Brazos Santiago Pass, is an important point for the shipping of petroleum products by barge and the receipt of barge shipments of sand and gravel. It has a large shrimp boat fleet, and the town is widely patronized as a resort for sport fishing and recreation.