The dry season from July to September is generally the best time to visit. River visibility is at its peak — the water in the Rio da Prata and Rio Sucuri is clearest when rainfall is low — and hiking to the waterfalls is more comfortable in the drier, cooler air. July is also Brazilian school holiday season, which means Bonito is at its busiest and most expensive; book accommodation and all activities well ahead if you come then.
The Gruta do Lago Azul is actually most vivid in January and February, when the angle of morning sunlight sends a shaft into the cave and illuminates the underground lake most intensely. The trade-off is that the rainy season (December–March) makes the rivers murkier and some trails harder going.
The Pantanal surroundings see more wildlife activity during the wet season, when water levels are high and animals concentrate around the floodplains. Many visitors combine Bonito with a Pantanal safari, and timing depends on which experience takes priority.