Reaching the Arquipélago dos Bijagós can be complicated, as the former ferry between the islands and Bissau no longer runs. A replacement ferry was said to be on its way from abroad.
Rough and risky canoas (motor canoe; per person CFA2500, six hours) make the journey. Schedules depend on weather and tides. Keep an eye on luggage that could unintentionally go missing when things are off-loaded at various stops.
Alternatively, contact a resort with a speedboat (a few on Bubaque and the two on Iiha Rubane) to see if you can secure a spot. Or head down to the pier in the morning to see if any speedboats are heading out. On good weather days in the high season, odds are you'll find a spot, if not on the first day, then the following day or the one after.
If heading to southern Guinea-Bissau, there's a daily ferry from the jetty around 500m east of Pidjiguiti across the river to Enxudé (CFA1500, two hours). There;s no set departure time; it's best to arrive in the morning or inquire the day before. From there, trucks are available for onward transport to Buba, Catió or São João.
Once in Bissau, you can get sept place taxis (Peugeot 504s with seven seats) and transporte misto buses to just about anywhere in the country at the gare routière (bus station), inconveniently located about 10km (CFA1000 by taxi) outside town.