The four main departments of the IVM are: Environmental Economics, Environmental Geography, Environmental Policy Analysis, and Water and Climate Risk. Each department has a clear focus in its research themes, but the departments also conduct joint research projects through IVM's Integrating Themes: climate, water, energy and ecosystems. The department staff closely collaborate in the BSC, MSc and PhD programmes, together with other research groups within the VU Amsterdam and the University of Amsterdam (UvA).

IVM is also closely affiliated with the department Environment and Health.