During South African school holidays (Christmas, Easter, August), southern Mozambique's coastal resorts fill up. Advance bookings are recommended, although you'll usually be able to find somewhere to stay.
May through September are generally the best months for diving around the Bazaruto Archipelago and elsewhere along the southern Mozambican coast.
During the height of the rains, in February and March, expect occasional tropical storms and flooding in parts of the south. Maputo, however, can be comfortably visited at any time of year.