The jaguar explains that the Inca people are endangered by malaria and European explorers, and the player will be taken back in time in order to search for cinchona and deliver it to the king.

The jaguar from the dream appears throughout the game as a hazy vision, running off a checklist of items desired by the Inca King, and offering various gloomy sentiments about the rainforest in general.

Players must navigate the treacherous waters of the Amazon to avoid hitting other boats, logs, and whirlpools or paddling up the wrong tributary, travel through the forest in search of exotic plants and animals to photograph and identify, use harpoons to fish in the river and then identify whether the catch is edible, and trade with the individuals encountered at the various stops along the river.

The player is given a good feel for the differing attitudes and clashing roles portrayed by the encountered individuals, pertaining to the history of the Amazon.

Upon reaching the hidden city in which the Inca are living, players are graded on various aspects of the game, including the amount of personal activity on the journey, the number of plants and animals correctly identified in the rainforest, whether or not they acquired additional gifts for the Inca King, and, depending on the version of the game, the amount of time taken, the health of the player, and the completion of mini-quests.

[3] The game helps players develop comprehension, survival and navigation skills, without any complicated tasks required and quest clues to follow.

[4] Computer Gaming World in 1993 warned of The Amazon Trail's "severe" hardware requirements, but approved of the "entertaining adventure's ... splendid animation and authentic native music", and its teaching of planning, research skills, and history.