Background Schistosoma haematobium is the most widespread schistosome species in Senegal and occurs in several regions of the country especially in the Sudan-Sahelian zone. The aims of the study were i) to determine the freshwater species ii) to ascertain the role of the identified snail species in the transmission of S. haematobium and iii) to study the impact of drought on the snails. Methods Snails were sampled each year in 17 sites from July to November-December 2012 and 2013. At each snail survey, snails were grouped by village, counted, identified according to shell morphology and the rates of schistosome cercarial shedding recorded. The shell height of the snails collected in July was measured and classified into four groups according to their size in order to determine those that are open to aestivation. Results B. senegalensis and B. umbilicatus were the only snails intermediate hosts collected in the Niakhar study area. B. senegalensis is found in all the 17 sampling sites while B. umbilicatus was only found in one site out of the many surveyed. The total number of B. senegalensis collected in 2012 and 2013 was 1032 and 8261 respectively. A total of 901 and 6432 B. senegalensis were tested for Schistosoma spp. infestation in 2012 and 2013 respectively. For B. umbilicatus, 58 snails were collected and tested in 2012. In 2013, 290 were collected and 281 tested. The overall rates of schistosome cercarial shedding were 0 % in 2012 and 0.12 % in 2013 for B. senegalensis and 13.79 and 4.98 % in 2012 and 2013 respectively for B. umbilicatus. For both species collected in July, size group 3 individuals (7–9.9 mm) were the most numerous, 63.6 and 57.8 % for B. senegalensis and B. umbilicatus respectively. B. umbilicatus was reported for the first time in the region of Fatick located in the old ecological zone of Sine-Saloum, is able to maintain Schistosoma spp. larvae during 7 months of drought and may transmit the disease in early July, increasing the period and the risk of transmission. Conclusion This study recommends an adaptation of snail control strategies at pond cycles and ecology of the snails in these seasonal foci. Malacological control strategies must take into account these phenomena of drought resistance and the capacity of some snails to maintain parasite during aestivation. The treatment of ponds with Bayluscide at the end of the rainy season in November and upon onset of rains in July would be more advantageous to the control of snails thereby reducing transmission of urogenital schistosomiasis in the Niakhar area.