The nearest airport is Campo Grande (CGR), the state capital, about 260 km to the northeast. Fly to Campo Grande from São Paulo (roughly 2 hours) or other major Brazilian cities, then continue to Bonito by road. The drive takes around 4.5 hours; the road has improved significantly in recent years though sections were unpaved until recently — check current conditions if hiring a car.
Organised transfers run between Campo Grande airport and Bonito, which is the easiest option if you are not hiring a car. Several agencies offer combined packages that pick you up at Campo Grande and route you through the Pantanal before arriving in Bonito, which makes good use of the journey. There is no rail service to Bonito. Intercity buses run the Campo Grande–Bonito route but they are slow and infrequent; most visitors use a transfer or rental car.