Microplastic contamination in coral reef environments is increasingly recognized as a global concern; however, the extent to which polymer composition can resolve contamination sources and transport processes remains poorly understood. In this study, we assessed the abundance, composition, and diversity of microplastics (< 300 µm) across multiple reef systems in the Cuban archipelago using high-resolution spectroscopic analysis. Microplastic abundance varied substantially among sites, with a median concentration of 66 particles L⁻¹ (IQR: 45–115 particles L⁻¹), ranging from 8 to 218 particles L⁻¹. A total of 11 polymer types were identified, with polyethylene (PE), polypropylene (PP), and polyamide (PA) dominating the assemblages and accounting for approximately 77% of detected particles. While these polymers were consistently observed across all sites, indicating a pervasive regional background signal, highly impacted reefs exhibited more complex polymer profiles, including the enrichment of polyurethane (PU), polytetrafluoroethylene (PTFE), and polyvinyl chloride (PVC), reflecting localized anthropogenic inputs. Multivariate analysis revealed distinct compositional groupings associated with different contamination regimes. Notably, some sites exhibited elevated microplastic abundances while remaining dominated by common polymers, indicating a decoupling between contamination levels and source-specific signatures. This pattern suggests that regional transport and mixing processes, including circulation through the Caribbean basin and the Yucatán Channel, play a major role in shaping microplastic distributions in reef environments. These findings demonstrate that polymer composition provides critical information beyond abundance alone, enabling the differentiation between source-driven contamination and transport-driven accumulation. The integration of polymer-specific analysis with abundance and diversity metrics offers a robust framework for improving source apportionment and informing monitoring and management strategies in coral reef systems.