Monitoring temporal trends in ecosystem functioning of protected areas (PAs) provides important knowledge of local and regional ecological responses to both environmental and anthropogenic drivers of change. Understanding such changes constitute a great global effort to preserve biodiversity and ecosystem services. We characterized the inter-annual trends of the enhanced vegetation index (EVI) seasonal dynamics in the PAs of southern Spain and northern Morocco. We used a time series of satellite images of the Moderate Resolution Imaging Spectroradiometer Terra sensor from January 2001 to December 2012. The EVI inter-annual trends were grouped into four patterns of trends. Patterns of trends in the EVI seasonal dynamics may be climate driven in the PAs of both countries. However, socioecological processes might be an additional underlying cause of the patterns of trends in the EVI seasonal dynamics of Moroccan PAs and Spanish wetland PAs. The use of remote sensing to monitor temporal trends in ecosystem functioning should be considered to understand the ecological responses to drivers of change in natural ecosystems.