The ERSD, together with the Chemical Sciences, Geosciences, and Biosciences Division of the DOE Office of Basic Energy Sciences have teamed with the National Science Foundation to establish several Environmental Molecular Science Institutes (EMSIs). The EMSI program is aimed at increasing the fundamental understanding of molecular-level process in natural environments, including those impacted by human activities. Five-year grants are awarded competitively to universities and National Laboratory partners. NSF funding is used to support the university researchers and DOE funding is used to support National Laboratory participation.   ERSD currently supports four EMSIs, based at the University of Notre Dame, the State University of New York at Stony Brook, Penn State University and Stanford University.

The mission of the Notre Dame Institute is to determine the effects of nano- and micro-particles (e.g., bacteria, natural organic matter, and mineral aggregates) on contaminant transport in geologic systems. The Institute blends the environmental science and engineering expertise and facilities of the university with those at Argonne,  Sandia, and Oak Ridge National Laboratories, as well as at DuPont Engineering Technology.
The mission of the Center for Environmental Molecular Science at SUNY Stony Brook is to develop a molecular-level understanding of the processes underlying contaminant sequestration in natural and engineered systems.  The Institute draws upon expertise in the critical disciplines of chemistry, geochemistry, physics, microbiology, and materials science at Stony Brook and Brookhaven National Laboratory.
The Center for Environmental Kinetics Analysis based at Penn State University  will examine molecular issues related to biogeochemical reaction kinetics and the cycling of elements at multiple scales in the environment. The goal is to provide a more fundamental understanding of the dynamics of biogeochemical processes in natural systems. This Center is a joint venture between Penn State University researchers and researchers at Lawrence Berkeley National Laboratory, Pacific Northwest National Laboratory and Los Alamos National Laboratory.
At the Stanford University Institute, the fundamental mechanisms of chemical and biological interactions at environmental interfaces will be examined at the molecular scale. The goal is to understand the structure of the electrical double layer at the solid-aqueous interfaces of metal oxide surfaces to understand the influence of microbial biofilms on reactions occurring at these interfaces. The Stanford Environmental Molecular Science Institute involves university researchers from across the country as well as researchers from Lawrence Berkeley National Laboratory and Pacific Northwest National Laboratory.