The potential impact of irrigated agriculture on water-related vector-borne diseases has been an increasing source of concern for researchers from the bio-medical sector. While most research on the potential impacts of irrigation on the health of local populations focuses on vector densities, levels of exposures, health services and technologies (prophylaxis, mosquito nets), we argue that it is essential to enlarge the scope of investigation and consider the complex mechanisms by which factors such as agriculture-generated changes in ecosystems, gender repositioning in the family organization as a result of access to new crops, and production activities combine together in increasing disease risks and producing new scenarios in the management of disease. This paper presents the results of an investigation of how transformations induced on the local society by the intensification of inland valley irrigated rice cultivation influence malaria health care systems and modulate risks to the health of local populations, within well-defined geographical boundaries in northern Côte d'Ivoire. Our results indicate that socio-economic transformations and gender repositioning induced, or facilitated, by the intensification of inland valley irrigated rice cultivation lead to a reduction of the capacity of women to manage disease episodes, contributing therefore to increase malaria incidence among farming populations.