The Mar Menor is a hypersaline coastal lagoon located in the southeast of Spain. This fragile ecosystem is suffering several human pressures, such as nutrient and sediment inputs from agriculture and other activities and decreases in salinity. Therefore, the development of an operational system to monitor its evolution is crucial to know the cause-effect relationships and preserve the natural system. The evolution and variability of the turbidity and chlorophyll-a levels in the Mar Menor water body were studied here through the joint use of remote sensing techniques and in situ data. The research was undertaken using Operational Land Imager (OLI) images on Landsat 8 and two SPOT images, because cloudy weather prevented the use of OLI images alone. This provided the information needed to perform a time series analysis of the lagoon. We also analyzed the processes that occur in the salt lagoon, characterizing the different spatio-temporal patterns of biophysical parameters. Special attention was given to the role of turbidity and chlorophyll-a levels in the Mar Menor ecosystem with regard to the programs of integral management of this natural space that receives maximum environmental protection. The objective of the work has been fulfilled by answering the questions of the managers: when did the water quality in the Mar Menor begin to change? What is happening in the lagoon? Is remote sensing useful for monitoring the water quality in the Mar Menor? The answers to these questions have allowed the generation of a methodology and monitoring system to track the water quality in the Mar Menor in real-time and space. The tracking system using satellite images is open to the incorporation of images provided by new multispectral sensors.