We designed and implemented participatory computer simulations in three workshops in New Zealand’s Upper Waikato catchment to learn how market-based instruments (MBIs) might improve freshwater outcomes when managing water and land resources within limits. An Excel-based platform was built to simulate, in stakeholder workshops, the use of transferable permits and user charges for both water quantity and water quality in the Upper Waikato catchment. Each participant managed a hypothetical property in a simplified catchment that included seven farms, a pulp mill, district council, and a hydro-electric company. Based on profit schedules and policy settings, participants made choices about production intensity, land use change and trading of water and/or nutrient allowances. The simulations highlighted the social and cultural context in which MBIs must operate, and how that context influences the outcomes that we can expect from MBIs. Participants found the simulations to be a valuable learning experience.