Abstract: Watershed-estuarine systems represent complex ecological network that extends from headwaters to estuaries and adjacent areas, encompassing rivers, lakes, wetlands, deltas, coastal marshes, and nearshore marine zones. In recent years, these ecosystems have faced severe ecological security issues, including water pollution, habitat fragmentation, ecosystem health deterioration, and biodiversity loss. These issues are primarily driven by urbanization, industrialization, agricultural activities, climate change, and infrastructure development, and have significantly constrained regional socio-economic development. Remote sensing (RS) and geographic information systems (GIS), as effective tools for modern ecological environment monitoring and management, offer extensive, high-resolution geographic, biological, and environmental data, significantly enhancing the accuracy and timeliness of ecological security assessments. This paper reviews the applications of RS and GIS technologies for assessing the ecological security of watershed-estuarine ecosystems, focusing on three key aspects: ecological health (EH), ecosystem service values (ESV), and ecological risk(ER), and outlines the main data sources and assessment models used in the integrated application of RS and GIS. Furthermore, the current state of RS and GIS application, challenges, and future directions for technological innovation and interdisciplinary collaboration are discussed. By integrating multi-source data and intelligent analysis, we aim to improve the scientific basis and practical effectiveness of ecological security assessments, providing a scientific basis for ecological protection and sustainable development.