Intensive livestock production in globalized supply chains has led to severe nutrient pollution of freshwater bodies with negative effects on ecosystems and drinking water supply. We argue in this chapter that responsible water management and sustainable livestock production can only be achieved if what is often reduced to a “nutrient problem” is addressed from a systemic perspective. This implies a transformative change in the whole food system. The chapter provides examples of innovative action and collaborative initiatives in innovation networks. It highlights that transformative change can only be achieved by multi-level governance where bottom-up initiatives are embedded and linked to national and international (EU) policy processes.