Phragmites australis populations in native areas have been gradually declining since the mid-20th century. We developed a logical approach based on remote sensing to monitor the conservation status of P. australis beds in response to environmental gradients and orient future management actions in Lake Garda (northern Italy). During the 2010 growing season we collected data on: (i) the structural and functional status of seven P. australis beds and (ii) land cover in a 50-m buffer around each bed, and we tested four different vegetation indices (VIs) derived from a multi-temporal and multisensor dataset. Double hierarchical clustering based on the VI statistics and environmental variables (morphological, functional and land-use) showed a good consistency between the outputs of the vigor-function analysis and the environmental classification of the P. australis beds considered. Overall, the bed's area was the most influential factor in the data clustering procedures, followed by the descriptors derived from the enhanced vegetation index. Our results confirmed the importance of temporal characteristics of remote sensing data to assess the conservation status of common reed beds and proved the sensitivity of VIs and derived descriptors to local environmental conditions within a homogeneous littoral area. This study supports the utility of remote sensing for monitoring riparian vegetation and analyzing the spatial and temporal response of P. australis populations to human pressure and management actions.