Artificial drainage is among the most widespread land improvements for agriculture. Drainage benefits crop production, but also promotes nutrient losses to water resources. Here, we outline how a systems perspective for sustainable intensification of drainage can mitigate nutrient losses, increase fertilizer nitrogen use efficiency (NUE) and reduce greenhouse gas emissions. There is an immediate opportunity to realize these benefits because agricultural intensification and climate change are increasing the extent and intensity of drainage systems. If a systems-based approach to drainage can consistently increase NUE while maintaining or increasing crop production, farmers and the environment will benefit.