Participatory modeling is the process of incorporating stakeholders, often including the public, and decision makers into an otherwise purely analytic modeling process to support decisions involving complex natural resources questions. Participatory modeling is particularly compatible with the rising focus on integrated water resources management, which incorporates systems theory and aims to protect and improve water resources while considering economic and social concerns in the community. In this article, we present a series of lessons based on experience working with stakeholder groups to develop watershed and water quality models to address water resource issues in Maryland, Vermont, Utah, and Virginia. We believe these lessons in participatory modeling, discussed from our perspective as scientists and modelers engaged in applied watershed issues, can help to achieve successful participatory modeling efforts elsewhere. The lessons relate to stakeholder engagement, modeling tools, model development and calibration, scenario testing, and applying results to management decisions.