The highlights of the Northern Pantanal can mainly be divided between two destinations.
The most popular destination in the Northern Pantanal is Porto Jofre, which is the base for visiting “Jaguarland”, the Encontro das Águas State Park. This is the best place in the World to see jaguars in the wild. The safaris are done on boat safaris on the Cuiaba, the Piquiri Rivers and their tributaries. Besides jaguars, you can easily see Capybaras, Yacare Caimans and close to 100 species of birds (including Hyacinth Macaws, Toco Toucans, Chaco Chachalacas, multiple Heron and egret species, 5 species of kingfishers and the iconic Jabirus) With some luck Giant River Otters and the Brazilian Tapir can be seen too. If you are interested in photographing jaguars this is the place to be.
Further North, 2-hours away from Cuiaba, there are some great lodges near the town of Pocone. Most of these lodges are huge conservation successes and you could explore a different habitat, the grasslands.
Here the most sought-after animals are Giant Anteaters, Crab-eating Foxes, Peccaries, and 6-7 raptor species along with Red-legged Seriema, the Greater Rhea.