The Galápagos Islands are one of the biggest marine reserves in the world, home to a complex dynamic between its inhabitants, tourists, and biodiversity. Therefore, control over the logistics surrounding the resulting human mobilization process is fundamental to minimize the impact on the Islands' natural resources. This research gathers relevant information regarding the operation of the maritime transportation system of the islands and the waste management of its floating population based on official sources as well as in-situ observation. This chapter includes three sections with the purpose of maximizing the range of information analyzed. The first section covers the maritime cargo transportation from the continent to the islands. The second one covers the transportation of people between the islands, and the third covers the transportation and management of waste produced by each island. The information covers the institutions and policies that govern each of the systems considered and can serve to optimize the transportation logistics of the Galápagos Islands.