Characters encountered include nasty Fleens and grouchy Norfs. Through a series of activities and mini-games, gameplay continues until all nine activities and rescues are complete. The surviving Zoombinis select either an upper path (color sequencing activity) or lower path (maze with hidden traps and magnets) to reach the next rescue site. Lost Zoombinis go back to the original selection screen, and losing more than eight requires the player to restart the level. At least eight must get through safely to advance to the next set of activities. Gameplay commences with three activities that focus on the sorting and logic skills needed to lead them across a river, through a pipe maze, and out of a trap. The full game mode requires gathering an initial rescue party of 16 Zoombinis, little round blue creatures who have distinguishing features such as eyes, noses, hairstyles, or shoes. A practice mode offers a manual choice of any level in any order.
Nine puzzle games, each with three levels of difficulty, default to the easiest level with automatic advancement after an activity has been successfully completed three times. Children ages eight and up solve logic and critical thinking puzzles in Zoombinis: Mountain Rescue, as they save the little creatures and their neighbors the Boolies from a fierce storm.