Superficial water bodies play a fundamental role in ecological and socioeconomic terms. Therefore, it is necessary to investigate methods to know which may be losing their persistence over time. In this manuscript, the methodology and main results of the spatial analysis process utilized for generating an area-based conservation indicator are presented. Binary monthly water-no-water layers were obtained from the processing of SAR Sentinel 1a images. A spatial layer of water bodies built with data from three decades served as a reference to obtain the indicators of change with respect to the area registered in this multi-year layer. Considering that the monthly indicator was calculated as a percentage of its area in the multiannual reference layer, the obtained results can be defined as long-term change indicators. It is concluded that some water bodies considered permanent in the multiannual reference layer did not cover, during the study period (2016–2018), the values of the area recorded in that layer, but that most remained close to those values. A 30% reduction in the area covered by these bodies in the reference layer was observed. Regarding temporary water bodies, these were detected with a reduction of more than 80% as compared to the value in the reference layer, which may be an indicator of their gradual loss process. The information generated can be used for management and conservation purposes at the regional and local levels of water bodies.