This paper proposes novel applications of Participatory Operational Assessment (POA), as a qualitative/empirical tool for bridging the research gap in our knowledge of Border Security, while supporting the mission of the U.S. Department of Homeland Security “to build in security, to ensure resilience, and to facilitate customs and exchange” (DHS 2017). Each year, global trade volume exceeds 10.3 billion tons of cargo, 90% of which is being carried by ships (UNCTAD 2017). U.S. transport networks alone import and export at least two billion metric tons of cargo, including 15 million sealed containers (CBP 2017a). The task of DHS/CBP in safeguarding the national borders and intermodal (sea, land & air) security becomes more crucial each year, as the flow of goods grows exponentially in positive correlation with the population growth, and trade agreements, such as the NAFTA agreement between the U.S., Mexico, and Canada. This paper demonstrates the development of a “Participatory Operational Assessment” instrument, where homeland security officials and industry stakeholders form a think-tank for resolving security and operational challenges on both sides of the border. Specifically, this scholarly research funded by the U.S. Department of Homeland Security demonstrates the benefits of establishing a Public/Private Advisory Board in order to identify security threats on both sides of the border. This is a timely research, as border security risks impose serious threats for homeland security, with geopolitical, economic and trade hindrances. The DHS and its Agencies (CBP, USCG, TSA etc.) have introduced numerous noteworthy initiatives, platforms and programs, including CSI, C-TPAT, TWIC etc. A number of working groups are also affiliated with the DHS, in order to address security, trade and travel issues. Inspired by the capabilities of these initiatives, this research has created a project-specific team of experts aiming to evaluate quantitative findings on border security, and offer best industry practices.