Amphibians and reptiles are the most threatened vertebrates by traffic, especially near ponds and wetlands. The main aim of this study was to examine seasonal and spatial patterns of amphibian and reptile road mortality in Special Nature Reserve “Obedska bara” (Serbia). We chose a road section of 4.2 km near the largest wetland in Serbia, with two different habitat types (forest-pond and agricultural area-pond). During 2018 (32 fieldwork days) and 2019–2020 (three control fieldwork days), we found 20,457 and 2231 road-killed animals, respectively. We recorded nine amphibian and eight reptile species. Amphibians (93%) were more vulnerable to traffic than reptiles (7%). The number of killed amphibians and reptiles varied between the seasons. Generally, amphibian roadkill was most frequent during the summer, whereas reptile roadkill was most frequent in spring and at the end of the summer. Furthermore, different roadkill patterns were observed during the examined months. In addition, we found that habitat type significantly affects the vulnerability of animals towards the roads. For both amphibians and reptiles, there were significant aggregations of roadkill, and most hotspots were located at the forest pond habitat type where mitigation measures must be applied (construction of tunnels and fences).