Agency Jurisdiction
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There are several agencies that could have jurisdiction over your project, but typically the Adirondack Park Agency (APA) will be the "lead" agency within the park. 

The NYS Department of Environmental Conservation (DEC), NYS Department of Health (DOH), NYS Department of Transportion (DOT) and NYS Department of Parks, Recreation and Historic Preservation (PRHP) can all be involved from the state level depending on the nature of the project. 

The US Army Corp of Engineers (USACE) can be involved if your project has the potential to affect a navigable water body.

In addition to the state and federal agencies above local town or village code enforcement will require Building Permits for most porojects.

DEC  - Water Bodies, Shorelines and Wetlands

DOH - Septic Systems

DOT - Right of Ways, Access Roads and Driveways

PRHP - Historic Areas and Archealogical Sites

USACE - Navigable Waters and Wetlands

LOCAL - Site Plan Review and Building Permits