In the face of environmental change, high-quality and fine-scale information is essential in order to monitor the highly dynamic environments on land and sea. While traditional approaches to data collection face a number of practical limitations, advanced technologies could supplement and further improve our efforts. Taking sea turtles as a modeling organism, we present a novel methodological framework for monitoring species by means of advanced technologies, including Unmanned Aerial Vehicles coupled with image and temperature sensors. Diverse monitoring protocols were refined through pilot studies conducted in both terrestrial and nearshore sea turtle habitats. Our approach focuses on the collection of information for critical biological parameters concerning species reproduction and habitat use, following the complex life cycle of the species. Apart from biological information, our framework encompasses also the collection of information on crucial environmental factors that might be changing due to current and future human-derived pressures, such as beach erosion and temperature profile, as well as highly important human activities such as recreational use within nesting beaches that could undermine habitat quality for the species. This holistic and standardized approach to monitoring using advanced technologies could foster our capacity for conservation, resolving difficulties previously addressed and improving the collection of biological and environmental data in the frame of an adaptive management scheme.