The aim of this study was to conduct a large-scale freshwater snail survey in Benin to assess the malacological diversity and the larval trematode infections with a focus on Schistosoma genus. We conducted 82 freshwater snail surveys in 35 sites ranked in 4 types and belonging to 9 out of 12 departments. Among 19,200 collected snails, 11 species of freshwater snails were identified. Four species of human schistosome transmitting snails, Bulinus forskalii, B. globosus, B. truncatus and Biomphalaria pfeifferi and seven species of non-human schistosome transmitting snails. Although B. forskalii and B. globosus were the most largely distributed snails, none of the Bulinus snails were found naturally infected by schistosomes. B. pfeifferi was found naturally infected by S. mansoni only in one site with a 0.56% prevalence. The most risky areas were Borgou and the four coastal departments. Preliminary contempory information on human schistosomiasis was provided from three different sites. Schistosoma haematobium was found with 57.1%, 96% and 100% prevalences (two of which were new records for this species in Benin) while S. mansoni was restricted to one site (Toho-Todougba) with 74.3% prevalence. Our data showed that both schistosomiasis haematobium and mansoni prevalences increased during the last nineteen years in Toho-Todougba site.