Precision agriculture has been at the cutting edge of research during the recent decade, aiming to reduce water consumption and ensure sustainability in agriculture. The proposed methodology was based on the crop water stress index (CWSI) and was applied in Greece within the ongoing research project GreenWaterDrone. The innovative approach combines real spatial data, such as infrared canopy temperature, air temperature, air relative humidity, and thermal infrared image data, taken above the crop field using an aerial micrometeorological station (AMMS) and a thermal (IR) camera installed on an unmanned aerial vehicle (UAV). Following an initial calibration phase, where the ground micrometeorological station (GMMS) was installed in the crop, no equipment needed to be maintained in the field. Aerial and ground measurements were transferred in real time to sophisticated databases and applications over existing mobile networks for further processing and estimation of the actual water requirements of a specific crop at the field level, dynamically alerting/informing local farmers/agronomists of the irrigation necessity and additionally for potential risks concerning their fields. The supported services address farmers’, agricultural scientists’, and local stakeholders’ needs to conform to regional water management and sustainable agriculture policies. As preliminary results of this study, we present indicative original illustrations and data from applying the methodology to assess UAV functionality while aiming to evaluate and standardize all system processes.