The main objective of this work is to present a novel methodology to assess the environmental, ecological, and conservation status of mid-latitude estuaries by means of an index-based method, EstuarIndex. The EstuarIndex is an integration of four sub-indexes, assessing the status of the main subsystems present on estuaries: sandy environments, dunes, tidal flats, and the drainage network. Each sub-index includes variables combining three types of factors: morphosedimentary and oceanographic factors, ecological factors, and management and protection factors. The environmental status is finally evaluated in five possible classes: (1) Very low, (2) Low, (3) Medium, (4) High, and (5) Very High, according to EU requirements for classifying the conservation status of habitats. Three pilot zones along the Spanish coast have been chosen for testing the method: San Vicente de la Barquera estuary (N Spain), Guadiana estuary (SW Spain), and Ebro River delta mouth (E Spain). They present different oceanographic and geomorphological conditions. The results obtained have proven that EstuarIndex is a suitable methodology for the application to other estuaries. The systematic application of EstuarIndex on broad time scales would allow evaluating the system trends, what seems key for implementation of more realistic restoration strategies, and it has a great potential as a tool for environmental management in natural protected areas. Furthermore, it may help in the detection of the most relevant site-specific vulnerabilities for long-term sustainability in response to both natural and artificial drivers.