Mahajanga is a seaport, the most important one in Madagascar after Toamasina. The marine terminal accommodates containerships and small (150 gross ton) general cargo freighters. Because of limited water depth at the wharf, only small ships can call at the terminal. Deeper-draft ships anchor off the terminal and transfer cargoes to and from barges, which move it to and from the terminal. Severe storms during December of 2006 damaged the bulkhead, allowing water to flow in and wash backfill out from under the terminal's paving blocks. The resulting collapse of pavement blocks has made operations at the terminal less efficient and reduced the storage space available. The largest and most valuable containerized export is frozen shrimp.
The city is located on the Betsiboka River, which then leads to Bombetoka Bay.
Mahajanga is a favorite tourist destination for both Malagasy tourists and international travelers, with beautiful beaches, a coconut-lined bordwalk (La Boru), and eight months of hot yet virtually rain-free weather.
The city has a sizeable muslim population. In 1977, it was the scene of ethnic unrest, forcing the evacuation of the Comorian minority living there.
In December 2006, a typhoon hit Mahajanga, causing significant damage to the port facilities and to some buildings located on or near the coast.