The SEAFLOWER Biosphere Reserve (SBR) is the largest Marine Protected Area in the Caribbean Sea and the second largest in Latin America. Marine protected areas are under pressure from various stressors, one of the most important issues being pollution by marine litter, especially plastic. In this study our aim is to establish the distribution pattern and potential sources of solid waste in the different marine/coastal ecosystems of the islands of Providencia and Santa Catalina (SBR), as well as assess any interconnections between these ecosystems. At the same time, the distribution characteristics of marine litter in the different compartments facilitated a more dynamic understanding of the load of marine litter supplied by the islands, both locally and externally. We observed that certain ecosystems, principally back-beach vegetation and mangroves, act as crucial marine litter accumulation zones. Mangroves are important hotspots for plastic accumulation, with densities above eight items/m2 (minimum 8.38 and maximum 10.38 items/m2), while back-beach vegetation (minimum 1.43 and maximum 7.03 items/m2) also removes and stores a portion of the marine litter that arrives on the beaches. Tourist beaches for recreational activities have a low density of marine litter (minimum 0.01 and maximum 0.72 items/m2) due to regular clean-ups, whereas around non-tourist beaches, there is a greater variety of sources and accumulation (minimum 0.31 and maximum 5.41 items/m2). The low density of marine litter found on corals around the island (0–0.02 items/m2) indicates that there is still no significant marine litter stream to the coral reefs. Identifying contamination levels in terms of marine litter and possible flows between ecosystems is critical for adopting management and reduction strategies for such residues.