In 2016 NOAA Fisheries released its National Ecosystem-Based Fishery Management (EBFM) Policy, affirming a commitment to support an ecosystem approach to management, applied at regional scales. As the agency endeavors to implement EBFM, there is an increasing need to engage resource managers and users in identifying relevant ecosystem drivers, risks, and trade-offs. To fulfill this need, the NOAA Southeast Fisheries Science Center initiated a series of participatory fisheries system modeling workshops with fishing communities along Florida’s Gulf coast. A major finding from this initiative was that water quality issues, and in particular harmful algal blooms known as “red tides,” are perceived to be major threats to sustainability of fisheries in the region. By leveraging resources and collaborating with state, federal, academic and private agencies, research has since been conducted to better understand the severe red tide events and their impacts on biological and human communities. The participatory modeling approach was effective for defining discrete EBFM issues that were highest priorities for additional research and management consideration. At the same time, the approach was effective for engaging both researchers and stakeholders, and building synergies such as public-private partnerships to work toward common objectives. We will discuss the strength of the participatory modeling approach for building partnerships and identifying information gaps, how the resulting response plan led to decision-relevant knowledge, and the prospects for improving upon this research effort in the future.