Background Schsistosomiasis is endemic in sub-Saharan Africa. It is transmitted by intermediate host snails such as Bulinus and Biomphalaria. An understanding of the abundance and distribution of snail vectors is important in designing control strategies. This study describes the spatial and seasonal variation of B. globosus and Bio. pfeifferi and their schistosome infection rates between May 2014 and May 2015 in Ingwavuma, uMkhanyakude district, KwaZulu-Natal province, South Africa. Methods Snail sampling was done on 16 sites once every month by two people for 30 min at each site using the scooping and handpicking methods. Snails collected from each site were screened for schistosome mammalian cercariae by the shedding method. The negative binomial generalised linear mixed model (glmm) was used to determine the relationship between abundances of the intermediate host snails and climatic factors [rainfall, land surface temperatures (LST), seasons, habitats, sampling sites and water physico-chemical parameters including pH and dissolved oxygen (DO)]. Results In total, 1846 schistosomiasis intermediate host snails were collected during the study period. Biompharia pfeifferi was more abundant (53.36%, n = 985) compared to B. globosus (46.64%, n = 861). Bulinus globosus was recorded at 12 sites (75%) and Bio. pfeifferi was present at 7 sites (43.8%). Biompharia pfeifferi cohabited with B. globosus at all the sites it was present. High numbers of Bio. pfeifferi (n = 872, 88.5%) and B. globosus (n = 705, 81.9%) were found between winter and mid-spring. Monthly rainfall showed a statistically significant negative relationship with the abundance of B. globosus (p < 0.05). Dissolved oxygen (DO) had a statistically significant positive relationship with the abundance of Bio. pfeifferi (p < 0.05) while (LST) had a statistically significant negative relationship (p < 0.05). More B. globosus (8.9%, n = 861) were shedding schistosome mammalian cercariae compared to Bio. pfeifferi (0.1%, n = 985) confirming the already documented high prevalence of S. haematobium in Ingwavuma compared to S. mansoni. Conclusion Results of this study provide updated information on the distribution of schistosomiasis intermediate host snails in the study area and contributes towards the understanding of the transmission dynamics of schistosomiasis at the micro-geographical scale in this area. Graphic Abstract

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