Temperate estuarine seagrass meadows are often spatially heterogeneous and dynamic over fine spatial scales due to fluctuations in light availability, temperature, nutrient availability, and salinity. They are also prone to disturbance by heat waves, large rainfall events and direct anthropogenic damage. Capturing and characterising spatiotemporal variability using traditional satellite remote sensing techniques is challenging due to the mismatch of spatial and temporal scales. Here, we demonstrate the use of an Unoccupied Aerial Vehicles (UAV) with a multispectral sensor as an alternative approach as it allows for very high spatial and temporal resolution mapping and monitoring of seagrass beds. A series of UAV-captured images from eastern Australian estuaries were used as the basis for developing mapping and monitoring techniques tailored for temperate estuarine seagrass beds. Unsupervised change detection, water column correction, and novel red-edge based indices were used to characterise changes in seagrass cover at high spatial and temporal resolutions. Findings from the UAV studies were translated to satellite images and analysed using spatial ecology techniques to characterise the spatiotemporal variability of temperate estuarine seagrasses in eastern Australia.