Schistosomiasis is a major neglected tropical disease in sub-Saharan Africa. This study compared the epidemiology of urinary schistosomiasis among children living in two distinct ecosystems in Mauritania: the Senegal River Basin (Trarza region) and the arid oasis areas (Adrar and Tagant regions). A cross-sectional study was conducted between February 2023 and February 2024 involving 856 children across 14 sites. Urine samples were collected from school-aged children and subjected to macroscopic and microscopic examinations. A questionnaire was administered to each child to determine sociodemographic factors. Environmental and geographical factors were documented in the localities. The prevalence rate of urinary schistosomiasis among children in the Senegal River Valley was 32.4%. In the oases zone, prevalences were 6.43% and 3.35% in Tagant and Adrar, respectively. Macroscopic hematuria was 29.1%, 6.04%, and 4.18% in Trarza, Adrar, and Tagant, respectively. The intensities of infection were 48.9, 6.43, and 40 eggs/10 mL in the Trarza, Adrar, and Tagant regions, respectively. Based on sex, prevalence was higher among boys in the Trarza and Tagant regions, while in Adrar, it was higher among girls. Prevalence among children using polluted water sources with dense vegetation in the department of Tékane, in the Trarza region, was significantly higher (35.7%) than among those using cleaner water sources (21%). Urinary schistosomiasis remains highly prevalent among children living along the Senegal River, while considerably lower transmission was observed in oasis settings. These findings highlight the strong influence of environmental and water-related factors on transmission dynamics and underscore the need for targeted, context-specific control strategies.