Sea kayaking along the Manuel Antonio coastline offers a perspective on the park's sea cliffs and coves that you cannot get on foot. The Punta Quepos headland has interesting rock formations, and paddling into the sheltered bays at low tide gives access to beaches that the park trails do not reach.
Half-day guided tours are run by several operators based near the park entrance. The water is generally calm in the mornings; wind picks up in the afternoons. Monkeys, iguanas, and shore birds are regularly spotted from the water, and white-tip reef sharks are occasionally visible through the clear surface. No kayaking experience needed for the standard tours.