Maine’s Lower Penobscot River Watershed (LPRW) has gained national attention for river restoration efforts and threats from rising development pressures. Here, we describe an alternative futures modeling approach for the 2.5-million-acre watershed designed to foster interdisciplinary research, stakeholder engagement, and on-the-ground solutions to complex sustainability challenges. We use focus groups and Bayesian Belief Networks to integrate expert knowledge and spatial data to arrive at land suitability rankings for four important land uses: development, conservation, forestry, and agriculture. We then overlay these uses to identify areas of future conflict and compatibility across the landscape in an effort to foster greater collaboration and improved land use. Future work includes the co-development of stakeholder-derived futures scenarios, and the identification of sub-watersheds where future development may degrade water quality and cross regulatory thresholds for urban-impaired streams, resulting in significant mitigation and compliance costs.