It's worth contacting both the lodge and a tour operator and comparing prices. Often (though not always) the tour operator can offer a lodge package with airport pickup and transfers for the same cost or less than you might get booking directly with the lodge.
Located in Campo Grande, Brazil Nature Tours (tel. 067/3042-4659 or 9258-6581; www.brazilnaturetours.com) has some excellent packages for the Pantanal, for Bonito, and for combinations of the two. The agency is quick in responding to e-mail.
If you're just interested in the Pantanal, a 4-day, 3-night package tour at a Pantanal lodge including all meals and activities, with transfer from and to Campo Grande airport, starts at US$800 per person. Trips to Bonito include admission to a few of the most popular activities, such as a visit to the blue lake cave and snorkeling on the Rio Sucuri. A 4-day, 3-night Bonito trip starts at US$650 per person, including accommodations and transfers from and to Campo Grande. A 6-day, 5-night combo tour, with a 3-night stay in the Pantanal and a 2-night stay in Bonito, including all transfers, starts at US$1,330 per person. Mostly geared toward backpackers, Pantanal Trekking Tour, Rua Jaoquim Nabuco 185, Campo Grande (tel. 067/3042-0508; www.pantanaltrekking.com), offers more rustic 3- to 5-day overland trips through the Pantanal -- mostly along the Estrada Parque, a dirt road through the South Pantanal -- between Campo Grande and Corumbá. Trips include guides and activities such as horseback riding. Price depends on itinerary and number in group, but starts at about R$250 per day per person.
Note: This information was accurate when it was published, but can change without notice. Please be sure to confirm all rates and details directly with the companies in question before planning your trip.