Background: Greek islands face mounting pressures on their marine water resources due to tourism growth, agricultural runoff, climate change, and emerging pollutants. Safeguarding seawater quality is critical for ecosystem integrity, public health, and the sustainability of tourism-based economies. Objectives: This scoping review synthesizes and evaluates the existing research on seawater quality in the Greek islands, with emphasis on pollution sources, monitoring methodologies, and socio-environmental impacts, while highlighting the gaps in addressing emerging contaminants and aligning with sustainable development goals. Methods: A systematic literature search was conducted in Scopus, Google Scholar, ResearchGate, Web of Science, and PubMed for English- and Greek-language studies published over the last two to three decades. The search terms covered physical, chemical, and biological aspects of seawater quality, as well as emerging pollutants. The PRISMA-ScR guidelines were followed, resulting in the inclusion of 178 studies. The data were categorized by pollutant type, location, water quality indicators, monitoring methods, and environmental, health, and tourism implications. Results: This review identifies agricultural runoff, untreated wastewater, maritime traffic emissions, and microplastics as key pollution sources. Emerging contaminants such as pharmaceuticals, PFASs, and nanomaterials have been insufficiently studied. While monitoring technologies such as remote sensing, fuzzy logic, and Artificial Neural Networks (ANNs) are increasingly applied, these efforts remain fragmented and geographically uneven. Notable gaps exist in the quantification of socio-economic impact, source apportionment, and epidemiological assessments. Conclusions: The current monitoring and management strategies in the Greek islands have produced high bathing water quality in many areas, as reflected in the Blue Flag program, yet they do not fully address the spatial, temporal, and technological challenges posed by climate change and emerging pollutants. Achieving long-term sustainability requires integrated, region-specific water governance linked to the UN SDGs, with stronger emphasis on preventive measures, advanced monitoring, and cross-sector collaboration.