This paper intends to contribute to the debate on gender equality and water within the Sustainable Development Goals SDGs 5 and 6. Farmers organizations are often considered key stakeholders whose participation should be fostered to achieve a good water governance in agriculture and irrigation programs. Nonetheless, many water management interventions tackle participation as an instrumental and formal process. A common assumption is that granting sufficient space for women in water management will automatically ensure a greater gender empowerment. Nevertheless, often low importance is given to assessing who really actively participates and benefits from water development projects, favoring the technical aspects. This paper addresses the articulation between gender, water management and indicators, using male, female and mixed farmer organizations as touchstones in three regions of Senegal. The authors defines a system of water gender indicators grouped into five sections. The first results show more similarities between mixed and female organizations, while the main gender inequalities are visible in the water technique and economic domains. Thanks to this study, we can see how a gender-based analysis may allow to more deeply understand some more or less "hidden" water governance mechanisms and their related implications in terms of project management and policy making.