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There is a growing recognition that programs that seek to change people’s lives are intervening in complex systems, which puts a particular set of requirements on program monitoring and evaluation. Developing complexity-aware program monitoring and evaluation systems within existing organizations is difficult because they challenge traditional orthodoxy. Little has been written about the practical experience of doing so. This article describes the development of a complexity-aware evaluation approach in the CGIAR Research Program on Aquatic Agricultural Systems. We outline the design and methods used including trend lines, panel data, after action reviews, building and testing theories of change, outcome evidencing and realist synthesis. We identify and describe a set of design principles for developing complexity-aware program monitoring and evaluation. Finally, we discuss important lessons and recommendations for other programs facing similar challenges. These include developing evaluation designs that meet both learning and accountability requirements; making evaluation a part of a program’s overall approach to achieving impact; and, ensuring evaluation cumulatively builds useful theory as to how different types of program trigger change in different contexts.