The South Atlantic Division does a wide variety of environmental work across the whole spectrum of its mission. On the military side, the division assists the Army and Air Force with environmental studies, remediation, and clean-up of hazardous and toxic material. It assist them in properly accommodating endangered species and in evaluating the environmental impacts of contemplated actions. Under its Formerly Used Defense Sites (FUDS) program, the division acts as the federal agent to identifying and removing dangerous chemicals and ordnance from sites previously used by the armed forces for training or development.

On the water resources side, the division incorporates environmental concerns in virtually all of its actions, from operation of reservoirs to construction of multiple-purpose projects. In addition, the division is authorized to build environmental restoration projects which specifically seek to correct past environmental degradation. The Kissimmee River Restoration Project and Everglades Restoration are two of the largest and most ambitious environmental restoration projects in the world.