The Habitat Agency was formed in May 2013 and has a major role in implementing the Habitat Plan, which was developed by the Santa Clara Valley Transportation Agency, Santa Clara Valley Water District, County of Santa Clara, and the Cities of Gilroy, Morgan Hill, and San Jose. The Habitat Plan covers about 2/3 of the area of Santa Clara County. The Habitat Plan provides streamlined state and federal permitting for public and private projects, while offering a comprehensive and effective way to address impacts of those projects on endangered and threatened species and their habitats. The most significant role of the Habitat Agency is to acquire and manage a Reserve System that will serve as mitigation for project impacts and contribute to the recovery of the species covered by the Habitat Plan.

The Habitat Agency is responsible for executing the requirements of the Habitat Plan, the permits, and the Implementing Agreement. The Habitat Agency coordinates with science advisors, outside consultants, and other land management agencies to ensure adequate and coordinated Habitat Plan implementation. The Habitat Agency includes, as part of staff or contract resources, a network of scientists, administrators, and other specialists that oversee and carry out planning and design, habitat restoration, monitoring, and adaptive management programs. The Habitat Agency is a Joint Powers Authority (JPA) composed of the Cities of Gilroy, Morgan Hill, and San Jose, and Santa Clara County. The JPA is limited to the four participating jurisdictions because the Joint Exercise of Powers Act requires that a JPA can only exercise powers held by all the participating agencies. Of the participating agencies, only the four jurisdictions have the authority to adopt the Habitat Plan fees. Because all of the Permittees are responsible for implementing the Habitat Plan, all of the Permittees have a role in the Habitat Agency. The Habitat Agency has two decision-making bodies, a Governing Board and an Implementation Board.