The Common Toad Bufo bufo is the amphibian with the highest rates of road mortality in many European countries. This elevated incidence of road kills has frequently been associated with migration to breeding sites. In this study, we analysed the mortality of the Common Toad in the road network in Catalonia (NE Spain), and investigated the related causative factors on four roads near a breeding site in the Pyrenees. Results suggest that the high mortality rate is due to a combination of factors: toad abundance, traffic density and quality of water bodies for breeding. On the road with the highest incidence of road kills we investigated whether deaths occurred at specific spots or in a random manner. The road was divided into 500 m sections and each section was classified according to biotic (type of vegetation) and abiotic (presence of streams, roadside topography) variables. Multiple correspondence analysis showed that sections with streams crossing under the road had the highest mortality rate, suggesting that such water bodies flowing into the breeding pond are the toads' main migratory pathways for hibernation and breeding. As toads use the same migratory routes each year, it is critical to identify areas with a high potential mortality so that efficient measures can be designed to increase wildlife permeability, and thereby reduce habitat fragmentation. This methodology could be applied in other areas with high amphibian mortality.