The EMSL is a national Department of Energy user facility operated by Batelle's Pacific Northwest Laboratories. The facility is designed to permit changes to laboratories simply and quickly without disruption of adjacent laboratories and central building utility systems. The nature of the research conducted at EMSL crosses many scientific disciplines and requires multidisciplinary design sensitivity facilitating collaboration not only between disciplines but also between theoretical and experimental scientists.

Research divisions encompass Macromolecular Structure and Dynamics, Materials and Interfaces Group, Environmental Dynamics and Simulation, Chemical Structure and Dynamics, Theory Modeling and Simulation, and Computer Information Sciences. Because of the high cost of constructing "hazardous occupancy" laboratory space, laboratory and non-laboratory spaces are carefully zoned in order to reduce construction costs.

The EMSL project contains radioactive materials zones. The exhaust air from these spaces is HEPA filtered prior to release to the atmosphere utilizing a specific radiation exhaust system with special filtering at the fan for all hoods in which isotopes are used.  The facility also houses a linear ion accelerator laboratory, which is used to analyze unknown waste chemical currently being stored in containers outside Hanford.