A challenging problem in the field of avian ecology is deriving information on bird population movement trends. This necessitates the regular counting of birds which is usually not an easily-achievable task. A promising attempt towards solving the bird counting problem in a more consistent and fast way is to predict the number of birds in different regions from their photos. For this purpose, we exploit the ability of computers to learn from past data through deep learning which has been a leading sub-field of AI for image understanding. Our data source is a collection of on-ground photos taken during our long run of birding activity. We employ several state-of-the-art generic object-detection algorithms to learn to detect birds, each being a member of one of the 38 identified species, in natural scenes. The experiments revealed that computer-aided counting outperformed the manual counting with respect to both accuracy and time. As a real-world application of image-based bird counting, we prepared the spatial bird order distribution and species diversity maps of Turkey by utilizing the geographic information system (GIS) technology. Our results suggested that deep learning can assist humans in bird monitoring activities and increase citizen scientists’ participation in large-scale bird surveys.