Baseline assessments and monitoring of protected areas are essential for making management decisions, evaluating the effectiveness of management practices, and tracking the effects of global changes. For these purposes, the analysis of functional attributes of ecosystems (i.e., different aspects of the exchange of matter and energy) has advantages over the traditional use of structural attributes, like a quicker response to disturbances and the fact that they are easily monitored through remote sensing. In this study, we described the spatiotemporal patterns of different aspects of the ecosystem functioning of the Spanish national parks and their response to environmental changes between 1982 and 2006. To do so, we used the NOAA/AVHRR-GIMMS dataset of the Normalized Difference Vegetation Index (NDVI), a linear estimator of the fraction of photosynthetic active radiation intercepted by vegetation, which is the main control of carbon gains. Nearly all parks have significantly changed during the last 25 years: The radiation interception has increased, the contrast between the growing and nongrowing seasons has diminished, and the dates of maximum and minimum interception have advanced. Some parks concentrated more changes than others and the degree of change varied depending on their different environmental conditions, management, and conservation histories. Our approach identified reference conditions and temporal changes for different aspects of ecosystem functioning, which can be used for management purposes of protected areas in response to global changes.