The union has a unique structure, which includes a General Assembly that  allows full representation of all interested groups and local community committees.

• General Assembly: Sixteen representatives of NGOs (2 from each NGO) elected by their own institutions, participate in this decision-making body.
The general Assembly elects the NGO members to the Board of Directors, defines statues and approves the Budget; Decision-Making in General Assembly is by majority vote and meet half-annually or upon request.
• Board of Directors: the Board of Directors is composed of 9 members, elected from the NGOs community. Elections of the Board members are held every two years, they meet every two weeks.
• Regional Representation: Regional units are composed of a regional council, whose structure is similar to that of the Board of Directors. They operate as regional centers, helping to establish environmental priorities and evaluating the environmental programs and needs of the local community.
• The Office of the Executive Director: This office reports to the Board of Directors and the General Assembly. It is charged with managing the logistical aspects and consists of four departments: Administration, Technical Assistance, Institutional Development and Communication.
• Independent Auditor: this position reports to the GA and is responsible for auditing financial statements and monitoring the GUN-GEO financial activities.