The distribution of certain permissive intermediate snail host species in freshwater is a crucial factor shaping transmission of intestinal schistosomiasis, a neglected tropical disease that causes much human suffering in Africa. To shed new light on southern Malawi, where cases of intestinal schistosomiasis have been found, repeated malacological surveys were conducted in Chikwawa and Nsanje Districts in the Lower Shire Valley, to detect and to characterize populations of Biomphalaria, the intermediate host for intestinal schistosomiasis. Sampling took place across a total of 45 freshwater sites, noting water conductivity, pH, temperature, total dissolved salts (TDS) and geographical elevation. The presence or absence of snails was predicted upon physiochemical and environmental conditions in Random Forest modelling. Water conductivity, TDS and geographical elevation were most important in predicting abundance of snails with water temperature and pH of slightly less important roles. This first report of B. pfeifferi in the Lower Shire Valley enhances understanding of the environmental factors that strongly associate and allow prediction of its local distribution. This represents a useful step towards developing appropriate intervention strategies to mitigate intestinal schistosomiasis transmission.