Over the past few decades, scholars and practitioners working on gender and development issues have advocated for more in-depth analyses that explore and foster change in the social institutions that create and perpetuate gender inequalities. Gender integration approaches in a research and development context are thus not something new. However, mainstream agricultural research and development programs often apply a rather simple understanding of gender to the design of such approaches, resulting in poor implementation. The CGIAR Research Program on Aquatic Agricultural Systems uses gender-transformative approaches to help achieve the goal of enhancing development outcomes of resource-poor women and men and their families in a sustainable manner. This paper details the approaches the program utilizes and is beginning to implement in its five learning hubs, which are located in areas where dependence on aquatic agricultural systems is high. The paper provides guidance on how other programs could prepare themselves to design and operationalize gender-transformative approaches and highlights some early learning on their application.