Managing ecosystems for multiple ecosystem services and balancing the well-being of diverse stakeholders involves different kinds of trade-offs. Often trade-offs involve noneconomic and difficult-to-evaluate values, such as cultural identity, employment, the well-being of poor people, or particular species or ecosystem structures. Although trade-offs need to be considered for successful environmental management, they are often overlooked in favor of win-wins. Management and policy decisions demand approaches that can explicitly acknowledge and evaluate diverse trade-offs. We identified a diversity of apparent trade-offs in a small-scale tropical fishery when ecological simulations were integrated with participatory assessments of social–ecological system structure and stakeholders’ well-being. Despite an apparent win-win between conservation and profitability at the aggregate scale, food production, employment, and well-being of marginalized stakeholders were differentially influenced by management decisions leading to trade-offs. Some of these trade-offs were suggested to be “taboo” trade-offs between morally incommensurable values, such as between profits and the well-being of marginalized women. These were not previously recognized as management issues. Stakeholders explored and deliberated over trade-offs supported by an interactive “toy model” representing key system trade-offs, alongside qualitative narrative scenarios of the future. The concept of taboo trade-offs suggests that psychological bias and social sensitivity may exclude key issues from decision making, which can result in policies that are difficult to implement. Our participatory modeling and scenarios approach has the potential to increase awareness of such trade-offs, promote discussion of what is acceptable, and potentially identify and reduce obstacles to management compliance. Significance Environmental management inevitably involves trade-offs among different objectives, values, and stakeholders. Most evaluations of such trade-offs involve monetary valuation or calculation of aggregate production of ecosystem services, which can mask individual winners and losers. We combine a participatory, modeling, and scenarios approach to identify social–ecological trade-offs in a tropical fishery and the implications on well-being of different stakeholders. Such trade-offs are often ignored because losers are marginalized or not represented by quantification, and because the nature of underlying values may result in socially “taboo” trade-offs that pit incommensurable values against one another. A participatory modeling and scenarios approach can increase awareness of such trade-offs, promote discussion of what is socially acceptable, and potentially identify and reduce obstacles to compliance.