Using drones to count wildlife saves time and resources and allows access to difficult or dangerous areas. We collected drone imagery of breeding waterbirds at colonies in the Okavango Delta (Botswana) and Lowbidgee floodplain (Australia). We developed a semi-automated counting method, using machine learning, and compared effectiveness of freeware and payware in identifying and counting waterbird species (targets) in the Okavango Delta. We tested transferability to the Australian breeding colony. Our detection accuracy (targets), between the training and test data, was 91% for the Okavango Delta colony and 98% for the Lowbidgee floodplain colony. These estimates were within 1-5%, whether using freeware or payware for the different colonies. Our semi-automated method was 26% quicker, including development, and 500% quicker without development, than manual counting. Drone data of waterbird colonies can be collected quickly, allowing later counting with minimal disturbance. Our semi-automated methods efficiently provided accurate estimates of nesting species of waterbirds, even with complex backgrounds. This could be used to track breeding waterbird populations around the world, indicators of river and wetland health, with general applicability for monitoring other taxa.Remote Sens. 2020, 12, 1185 2 of 17 semi-automated methods. The former can be extremely labour-intensive and consequently expensive, particularly for large aggregations of wildlife [26], further complicated when more than one species is counted. Semi-automated methods, including the counting of animals from photographs (e.g., camera traps) and drone imagery, are increasingly being developed around the world [27]. These methods reduce the time required to count and process drone images [28], accelerating the data entry stage and encouraging the use of drones as scientific tools for management. Such benefits allow for real-time monitoring and management decisions and could, for example, assist in the targeted delivery of environmental flows for waterbird breeding events [29].Generally, semi-automated counting methods are most effective for species where there are strong contrasts against the backgrounds, particularly when background colours and shapes are consistent [28]. They can distinguish large single species aggregations on relatively simple backgrounds [30][31][32], up to sixteen avian species (numbering in the hundreds) on simple single colour backgrounds, such as oceans [33,34], or single species aggregations of hundreds of thousands on complex backgrounds [3].Development of flexible, repeatable and efficient methods, using open source software, is important in ensuring methods are applicable across a range of datasets [35,36]. Further, there are potential cost implications of processing data, given that some processing software can be expensive (i.e., compulsory licence fees, called 'payware' in this paper) and so are often only accessible to large organisations in high-income countries [37]. Open source software, or software with optional lic...