The National Park Service is mandated to preserve and protect the natural resources in parks for future generations. To meet this challenge, a variety of environmental factors must be considered in all park management actions. The impact on the quality of water, air, geological resources, and a number of ecological, biological, and physical processes is evaluated for all plans, proposals and projects at Fire Island National Seashore. 

Fire Island National Seashore preserves critical coastal habitat for many rare and endangered species, as well as migratory corridors for birds, sea turtles and marine mammals. Within its boundaries, the Seashore also protects vital coastal wetlands, essential to water quality, fisheries, and the biological diversity of coastal, nearshore and terrestrial environments.  

Many threats to a park's resources, such as air and water pollution or invasive species, often originate outside of park boundaries. Managing most national parks requires a partnership-based, ecosystem-wide approach. 

At Fire Island National Seashore—with significant cultural features and landscapes, the presence of 17 vital preexisting communities within park boundaries at one end and a federally designated wilderness area at the other end of the spectrum, all so close to major urban centers, and coupled with conflicting mandates from other land management agencies overseeing the same or neighboring resources—the park managers' ability to arrive at sound decisions can be further complicated.

However, the National Park Service is committed to protect, manage and administer the parks so there is no degradation of the values and purposes for which the area was established.

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Fire Island National Seashore's natural resources are managed according to the criteria found in the 2006 Management Policies, Chapter 4.