The Sustainable Groundwater Management Act (SGMA) is introducing significant changes in the way groundwater is governed for agricultural use. It requires the formation of groundwater sustainability agencies (GSAs) to manage groundwater basins for sustainability with the engagement of all users. That presents opportunities for collaboration, as well as challenges, particularly in basins with large numbers of agricultural water users who have longstanding private pumping rights. The GSA formation process has resulted in the creation of multiple GSAs in many such basins, particularly in the Central Valley. In case studies of three basins, we examine agricultural stakeholders' concerns about SGMA, and how these are being addressed in collaborative approaches to groundwater basin governance. We find that many water districts and private pumpers share a strong interest in maintaining local autonomy, but they have distinct concerns and different options for forming and participating in GSAs. Multilevel collaborative governance structures may help meet SGMA's requirements for broad stakeholder engagement, our studies suggest, while also addressing concerns about autonomy and including agricultural water users in decision-making.