Depths in the Sea of Abaco are generally a few metres, and shallow reefs and shoals can pose a serious hazard to navigation.

Despite these hazards, the sea is popular with boaters and is sometimes referred to as a 'marine highway', offering a sheltered passage through the Abaco Islands.

To the west it is bordered by Great Abaco Island, which forms a nautically impassable barrier for its entire length.

None of the islands which border it contribute appreciable quantities of surface runoff, which is part of the reason why its waters are extremely clear.

Beyond the eastern edge of the sea, in the Atlantic Ocean, the seafloor drops off rapidly, generally deepening more than 200 metres (650 feet) over a distance of only a few kilometres.

[6] The Sea of Abaco sits atop the Little Bahama Bank, a massive carbonate platform built up from the remains of millions of years of marine organisms, including corals and foraminifera.