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Background Researching a water-borne disease in the middle of the Sahara desert might not seem the most relevant concern. However, nomadic Sahelian pastoralists health concerns regarding their livestock and anecdotal reports about trematode infections of  Fasciola  spp. and  Schistosoma  spp. in desert-raised animals justified an exploratory study focusing on the lakes of Ounianga in Northern Chad. The aim was to test whether trematode parasites such as  Schistosoma  spp. occur in human populations living around the Sahara desert lakes of Ounianga Kebir and Ounianga Serir in northern Chad. Methods The study was carried out in January 2019 and comprised of three components. First, a cross sectional survey based on a random sample drawn from the population to detect infections with  S. haematobium  and  S. mansoni ; second, focus group discussions exploring disease priorities, access to health and health seeking behaviour; and third, surveying water contact sites for intermediate host snails. Samples of trematode parasites and snails were confirmed on species level by molecular genetic methods. For parasitological and malacological surveys descriptive statistics were performed. Qualitative data analysis included the full review of all transcripts, followed by a descriptive and explorative thematic analysis. Results Among 258 participants, the overall  S. haematobium  prevalence using urine filtration was 39.2% [95% confidence interval ( CI ): 33.5–45.1%], with 51.5% of the infected suffering from heavy infection. The intermediate host snail of  S. haematobium  ( Bulinus truncatus ) occurred at water contact sites near both study villages, revealing the potential for local transmission. Although a positive  S. mansoni  point-of-care circulating cathodic antigen (POC-CCA) test result was obtained from 8.6% (95%  CI  5.7–12.8%) of the samples, no intermediate host snails of  S. mansoni  were found, and the relevance of  S. mansoni  remains uncertain. Qualitative findings underline the importance of morbidity caused by urinary schistosomiasis, and the lack of access to diagnostics and treatment as a major health concern. Conclusions This research revealed a high prevalence of urinary schistosomiasis in the population living around the lakes of Ounianga in the Sahara, a United Nations Educational, Scientific and Cultural Organization (UNESCO) world heritage site in Chad. Despite the high public health importance of the associated morbidity expressed by the population, there is no access to diagnostics and treatment. Further work is needed to develop and test a context-adapted intervention. Graphical Abstract

High prevalence of urinary schistosomiasis in a desert population: results from an exploratory study around the Ounianga lakes in Chad