It's wise to exercise caution when considering boat travel between Bissau and Bubaque during heavy wind or rain.
Ilha de Bubaque is the gateway to the rest of the Bijagós, with the exception of Ilha de Bolama and the private resort islands. The former ferry Expresso dos Bijagos used to leave Bissau port for Bubaque every Friday, returning from Bubaque on Sunday. Exact departure times depended on the tide, but were generally between 9am and 3pm. A replacement ferry was supposedly on the way at the time of research.
On other days, your choice is between rough and risky canoas (motor canoe; per person CFA2500, six hours) and a speedboat (per four-seater boat CFA150,000 to CFA250,000, 1½ to two hours).