Considering the present and future of the resources of the Hillsborough River is the Hillsborough River Interlocal Planning Board, an organization consisting of three elected officials representing the geographic location of the river. It is supported by the Hillsborough River Technical Advisory Council, comprised of eight agency representatives and three citizen members. Mandated by state law, the River Board and Council developed a Master Plan for the Hillsborough River, incorporating policies broadly pertaining to:

Water quality and quantity.
Safety and use of the river.
Protection of wildlife and its habitat and along the river.

The River Board and Council coordinate the plan's implementation between the jurisdictions along the river. Appropriate portions of the plan were adopted by the local jurisdictions as part of their respective Comprehensive Plans.