The scientific priorities of the Southwest CSC are driven by the needs and priorities of the natural and cultural resource management communities in the Southwest region, as contained in the Southwest CSC Science Agenda and as approved by the Southwest CSC Stakeholder Advisory Council (SAC).

Each CSC will have a Science Implementation Panel (SIP) to oversee peer review of all proposed projects and to recommend how to utilize available scientific assets to best address regional science priorities. To maintain high quality research, avoid conflicts of interest and protect confidential information, the SIP will implement rigorous procedures for reviewing proposals. The SIP will be chaired by the Southwest CSC Center Director.

CSC research agendas will also be reviewed from a national perspective to identify issues benefiting from multi-region collaboration among CSCs.