With climate change and urban development, water systems are changing faster than ever. Currently, the ecological status of water systems is still judged based on single point measurements, without taking into account the spatial and temporal variability of water quality and ecology. There is a need for better and more dynamic monitoring methods and technologies. Aquatic drones are becoming accessible and intuitive tools that may have an important role in water management. This paper describes the outcomes, field experiences and feedback gathered from the use of underwater drones equipped with sensors and video cameras in various pilot applications in The Netherlands, in collaboration with local water managers. It was observed that, in many situations, the use of underwater drones allows one to obtain information that would be costly and even impossible to obtain with other methods and provides a unique combination of three-dimensional data and underwater footage/images. From data collected with drones, it was possible to map different areas with contrasting vegetation, to establish connections between fauna/flora species and local water quality conditions, or to observe variations of water quality parameters with water depth. This study identifies opportunities for the application of this technology, discusses their limitations and obstacles, and proposes recommendation guidelines for new technical designs.