Remote sensing has been used from the 1980s to study inland water quality. However, it was not until the beginning of the twenty-first century that CHRIS (an experimental multi-angle sensor with good spectral and spatial resolutions) and MERIS (with good temporal and spectral resolutions) started to acquire imagery with very good resolutions, which allowed to develop a reliable imagery acquisition system so as to consider remote sensing as an inland water management tool. This paper presents the methodology developed, from the field data acquisition with which to build a freshwater spectral library and the study of different atmospheric correction systems for CHRIS mode 2 and MERIS images, to the development of algorithms to determine chlorophyll-a and phycocyanin concentrations and bloom sites. All these algorithms allow determining water eutrophic and ecological states, apart from generating surveillance maps of toxic cyanobacteria with the main objective of Assessment of the Water Quality as it was used for Monitoring Ecological Water Quality in smallest Mediterranean Reservoirs integrated in the Intercalibration Exercise of European Union Water Framework Directive (WFD). We keep on using it to monitor the Ecological Quality Ratio (EQR) in Spain inland water.