Nowadays the proliferation of small unmanned aerial systems or vehicles (UAS/ Vs), formerly known as drones, coupled with an increasing interest in tools for environmental monitoring, have led to an exponential use of these unmanned aerial platforms for many applications in the most diverse fields of science. In particular, ecologists require data collected at appropriate spatial and temporal resolutions to describe ecological processes. For these reasons, we are witnessing the proliferation of UAV-based remote sensing techniques because they provide new perspectives on ecological phenomena that would otherwise be difficult to study. Therefore, we propose a brief review regarding the emerging applications of low-cost aerial platforms in the field of environmental sciences such as assessment of vegetation dynamics and forests biodiversity, wildlife research and management, map changes in freshwater marshes, river habitat mapping, and conservation and monitoring programs. In addition, we describe two applications of habitat mapping from UAS-based imagery, along the Central Mediterranean coasts, as study cases: (1) The upper limit of a Posidonia oceanica meadow was mapped to detect impacted areas, (2) high-resolution orthomosaic was used for supporting underwater visual census data in order to visualize juvenile fish densities and microhabitat use in four shallow coastal nurseries.