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In developing countries, efforts to face food insecurity were revealed by construction of dams and hydro-agricultural managements. This study aimed to establish sanitary consequences in a hydro- agricultural zone. Methods: Data from 1847 children were analysed. Kato-Katz and concentration in MIF were used for intestinal parasites; research of microscopic haematury was used for urinary schistosomiasis. Nutritional status was estimated by WHZ and HAZ indexes. Association between malnutrition and independents variables was measured in univariate and multivariate analysis. Results: Among children, 80.1% were infested by at least one parasite, 30.8% by S. mansoni and 49.6% by S. haematobium. Prevalence of emaciation and prevalence of stunting were respectively, 32.6% and 25.5%. In the multivariate analysis: Age: (1 - 3 y age group, OR = 2.92, 4 - 6 y age group OR = 1.85, p < 0.001); S. mansoni (OR = 1.27, p < 0.027) and S. haematobium (high OR = 1.53, low OR = 1.44, p = 0.008), were associated with emaciation. Age: (4 - 6 y age group, OR = 1.78, 7 - 11 y age group OR = 2.55, p < 0.001) and S. haematobium (high OR = 1.58, low OR = 1.28, p = 0.005), were associated with emaciation. Conclusion: Development of bilharziasis (urinary and intestinal) with increased morbidity and malnutrition, attenuate benefits expected from hydro-agricultural managements. It is important to invest in the control of water-related diseases, which are amplified by hydro-agricultural managements.