The National Policy Statement on Freshwater Management now requires that water quality objectives and limits be set for all water bodies in New Zealand. Where objectives result in the development of nitrate limits for waterways and development pressure is likely to make these limits difficult to achieve, systems are needed to avoid over-allocation. This paper proposes a multi-level governance model for managing this load over time, with a focus on community self-governance and building a flexible system for managing leaching risk, given the very high levels of uncertainty in linking nutrient losses to objectives.