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Introduction The conservation and restoration of water-related ecosystems are central to achieving Sustainable Development Goal 6 (SDG 6), particularly Target 6.6. Despite the growing body of research on water resource management, the extent to which conservation strategies are being studied, implemented, and aligned with SDG 6.6 remains insufficiently synthesized. This study aims to systematically review the protection methodologies applied to conserve and restore water-related ecosystems and to identify research trends, policy approaches, and existing knowledge gaps. Methods A systematic review was conducted following the PRISMA framework. A total of 75 articles were initially retrieved from the Web of Science, Scopus, and ScienceDirect databases. After applying inclusion and exclusion criteria, 40 peer-reviewed studies were selected for detailed analysis. The selected literature was examined through a structured comparative synthesis focusing on ecosystem types, conservation strategies, governance and policy instruments, and the use of technologies and monitoring tools. Results The results show that conservation efforts are unevenly distributed across ecosystem types, with forests and wetlands receiving the greatest research attention, while aquifers and river systems remain significantly underrepresented. Commonly reported strategies include watershed reforestation, wetland restoration, environmental education initiatives, and remote monitoring technologies. However, many studies show limited alignment with specific SDG 6 targets and frequently lack detailed water quality assessment and monitoring indicators. Discussion The review reveals persistent structural challenges affecting the implementation of conservation strategies, including governance limitations, insufficient funding, technological gaps, and global inequalities influencing water resource management outcomes. These findings highlight the need to strengthen integrated planning, improve monitoring systems, and promote more balanced research attention across all water-related ecosystems. This study synthesizes current conservation approaches within the SDG 6.6 framework and identifies key knowledge gaps that can inform future research, policy development, and decision-making in water resource management.