Management of protected areas in the current context of global change requires approaches to characterize and to monitor ecosystem functioning. Remote sensing provides adequate tools for that because it provides índices that inform repeatedly and for large areas of land, about matter and energy exchanges between the biota and land surface. Considering this principle, and the continuous improvements in the availability of satellite data of higher quality and friendly use, we have developed with the Autonomous Organization of National Parks of Spain (OAPN), a monitoring system that complements other monitoring initiatives from this agency to inform about the conservation status of national parks. The system, called REMOTE, is based on the most used spectral vegetation indices on scientific literature, EVI (Enhanced Vegetation Index) and NDVI (Normalized Difference Vegetation Index), derived from the time series of satellite images of the MODIS-Terra sensor. The systems allows to progress in identification of reference conditions to understand and predict ecosystems response against environmental perturbations or management actions, and their directional changes (trends) they are experiencing. Likewise, establishment of reference conditions helps to identify anomalies that warn of sudden changes in ecosystem functioning. The system uses as ecosystem functioning indicators three attributes related to the annual carbon gains (net primary production) by the canopy, their seasonality and phenology. In addittion, Remote has been designed and programmed on open and free software allowing future modifications and improvements in an easy way. The implementation of this system aims to inform decision-makers and managers of the Network of National Parks of Spain about the health and conservation status of ecosystems.