Recently, due to rapid urbanization and industrialization, more roads are increasingly being built. As a result, the incidence of roadkill has increased for wildlife with reduced habitat, affecting both wildlife and humans. This study identified the patterns of water deer roadkill in Korea and predicted the rate of occurrence of water deer roadkill by city, county, and district based on roadkill locations. By analyzing the land cover around the water deer roadkill points, it was estimated that farmland was the most influential factor. The proportion of farmland in areas with frequent roadkill was higher than in areas without. It was found that water deer roadkill occurred frequently in places with low proportions of forests and natural grassland. Few or no instances of water deer roadkill occurred in areas with a high proportion of residential areas. Using MaxEnt, the predicted the value of water deer roadkill by city, county, and district in the Yeongnam region was derived. It was found that the northwest region of Gyeongsangbuk-do was the most vulnerable area to water deer roadkill. Regarding the coverage rate of paddies, fields, and orchards related to farmland, the difference between the top 10 regions and the bottom 10 regions predicted for roadkill was most pronounced. This study identified the main factors affecting water deer roadkill and predicted the vulnerable areas of water deer roadkill. If the limitations of this study are supplemented and roadkill prediction results are derived for various species by expanding the target site and adding target species, the results can be used to inform wildlife protection strategies and prevent casualties.