High quality research informed by systems thinking can contribute to positive outcomes in complex, dynamic situations related to managing natural resources such as water. This chapter refers to social-ecological systems thinking to identify characteristics of high quality transdisciplinary research that makes a lasting impact. We primarily draw on lessons from a four-year research for development project that focused on learning how to improve groundwater management in Pakistan. Uncontrolled and unmonitored use of groundwater for irrigation has resulted in declining water levels in parts of Punjab, Sindh and Balochistan. The project sought to address this by developing and supporting professional relationships among groundwater managers from government agencies, university researchers and farming communities. Six in-depth case studies, two from each province, enabled groundwater monitoring capacity, and understanding of the social and economic aspects of water use, to be developed together. Stakeholder forums ultimately developed as platforms for co-learning and collaborative planning around on-farm interventions and mobile applications. In this chapter we present the background literature that informed us, and what we did. We also reflect on what could be improved in similar future projects. We note the constraints of short term project funding on this type of collaborative learning based project, and highlight where structured and consistent investment in water resources planning is required. We also suggest that projects such as this would be improved by incorporating ecological perspectives alongside technical, social and economic aspects.