Emissions trading and nutrient trading interact in critical ways. The agricultural sector is a major emitter of both nutrients and greenhouse gases in New Zealand. Thus the simultaneous implementation of such systems will have a large impact on the farmers in affected catchments. Many of the mitigation options that are available to farmers, for example reducing animal numbers, will reduce both nutrient loss and greenhouse gas emissions. Thus the combined cost of control could be much less than the sum of the costs of the separate systems. The allocation of units under each system will also affect the same people. Monitoring systems for each pollutant could have common elements but could also impose a double burden. The interactions between the two systems will complicate the decision making process for farmers and need to be considered when the policies are designed so they are as complementary as possible.