The metabolism of urban systems produces waste that generates a negative impact on the environment. This dynamic is even more problematic in contexts of high ecological value such as Galapagos, where poor waste management can irreversibly compromise the ecosystem. This research work develops a material flow analysis in Santa Cruz - the most anthropized island of the Galapagos - particularly deepening the formal and informal waste flows in the local system. The study highlights a complex scheme of exchange of materials, where the public and private waste management system integrates informal practices that often strengthen the overall efficiency of the system. The analysis also suggests strategies and actions to improve recycling mechanisms on the island, in addition to proposing to replicate this type of study in diverse contexts, as it is a useful tool to optimize the use of resources at the local level and reduce the environmental impact.