Monitoring waterbirds is fundamental to understand the health status of wetland habitats. However, this monitoring has to be conducted by means of reliable data collection that can provide accurate information on population trends. Usually, waterbird monitoring is difficult, as nesting grounds are usually located in inaccessible reedbed, and by eye detection of cryptic species is hard. Drones have the capacity to overcome most of these problems, as they can provide with an aerial view of places otherwise unreachable, while reducing the disturbance and time spent in the field. The present study aims to compare the accuracy, disturbance levels, and managerial efficiency between ground (traditional) and drone counts of a cryptic species, the Purple Heron Ardea purpurea. Traditional monitoring methods were only capable of detecting 35% of the nesting pairs detected by the drone surveys (8.0 ± 11.8 versus 22.9 ± 38.2 nesting pairs in ground and drone surveys, respectively). Consequently, colony size estimates between methods showed poor agreement, to the point that traditional methods missed colonies otherwise detected by the drone. No apparent negative effects on nesting pairs where found when flying the drone. In addition, mean time spent to survey breeding sites with a drone was far less than with the traditional approach, down to a six-fold time reduction. This reduction, together with a lack of disturbance observed when conducting the drone monitoring, and an increasing monitoring precision and accuracy, supports the use of drones as the least invasive option for studies on population monitoring on hardly accessible sites.