Livelihood and water-related diseases are strongly linked to wetland management. The majority of wetland stakeholders in the Inner Niger Delta, Mali considered human health and sanitation the most important criteria of a list of challenges and water-related pressures. Yet, a methodology to integrate health risks and opportunities into wetland management plans has previously not been proposed, despite the clear links and substantial real-life challenges. In this paper, a framework is presented to do this in data-poor context structured around the process to evaluate and prioritise the appropriateness of management options to improve human health. In the data-poor context of the Inner Niger Delta, the selection of criteria and indicators, and the scoring of management options against these criteria and indicators has been done by a panel of stakeholders. Criteria were chosen to reflect the often difficult conditions in which management options need to be implemented and thus focused on the effectiveness and feasibility of management options to reduce the disease burden and the two major pathways for environmental disease transmission, namely contaminated water (pathogens) and stagnant water (parasites and organisms that can transmit them) at three wetland scales: urban areas, urban wetland and rural wetland. The feasibility for the sustainable implementation of a management option refers to the required institutional capacity and is scored by means of the concept of “adaptive capacity”. The presented framework uses rapid assessment tools and simplified scoring methods and proved useful in explaining issues across sectors and scales, to promote mutual understanding and to achieve an integrated assessment of the appropriateness of management options.