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Because it's a sprawling region, you'd need at least eight days to do justice to Sonora. If you have just a few days, start at beachfront San Carlos. (You can drive the entire way, or fly into Hermosillo and drive from there.) The next day, take the easier three-hour drive to lovely Álamos. Spend a night in Hermosillo before taking a leisurely drive along the Río Sonora, stopping for the night in Ures or Arizpe. Make sure to take the 4-km (2½-mi) hike along the rutted road out of Aconchi to soak in the hot springs.
If you only have the weekend, cross the border from the United States and explore the Ruta de los Misiones. Spend the night in Bahía Kino and come back up the Ruta de Río Sonora to catch the ruins of Padre Kino's adobe mission you missed at Imuris and head home.