Mafia Island lies across the trade winds and experiences the north-east Kaskazi and south-east Kusi seasons. The Kaskazi usually starts at the end of November after a period of shuwali (calm) and short rains (vuli). The Kusi is the longer and windier period, running from early July through to mid-September. 

The best time to visit Mafia Island is from June to October and from December to March. 

October to the end of March is the best months for diving. But for non-divers the months between June and October offer the best weather, as January to March are more hot and humid. The heavy rains come in April-May, and shorter rains in November.

Whale sharks are best seen from early December through to March.