This special issue features 15 papers focused on the use of remote sensing as applied to various aspects of freshwater, estuarine and near-shore benthic ecosystems. The work described herein is diverse, ranging across spatial and temporal scales, and making use of optical, radar and lidar technologies. The need for this applied research has become more crucial by the day, as resource managers are faced with issues ranging from non-point source pollution to wetland destruction, invasive species, climate change and more. Routine monitoring and mapping of the changes taking place in these ecosystems enable managers to focus their efforts in time and space, and to prioritize their responses to the most pressing issues. The most compelling aspect of much of the research reported within these pages is that the best advances emerge from the combined use of technologies across the spectrum (literally) and across a range of spatial and temporal scales. No single issue threatening the health of these ecosystems can be addressed using a single approach or with a single image acquired at a given point in time. Despite the additional resources and expense required to make use of multi-sensor, multi-temporal and multi-scale image data, the utility of such data becomes evident across a diverse range of ecosystems and a wide range of conditions. As such, we view this compilation as useful not only for applied resource management, but also as a compelling contribution to the advancement of both basic and applied research in this subject area.