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Water quality trading programs envision regulated point sources meeting discharge control requirements and then being allowed to increase their nutrient discharge if they secure nutrient reduction credits from other pollutant sources in the watershed. Reduction credits can be created when agricultural land managers implement best management practices and regulators predict that those practices will result in water quality conditions equivalent to controlling discharges at the regulated source. However, natural variability in runoff combines with model and data limitations to make predictions of water quality equivalence uncertain. Nutrient assimilation credits can be created by increasing the capacity of the ecosystem to assimilate nutrients through investments in aquatic plant biomass creation and harvest, shellfish aquaculture, stream restoration, and wetlands restoration and creation. Nutrient assimilation credits can provide greater certainty than agricultural best management practices that trading will result in equivalent water quality. Such credits should be an option in trading programs.