As human activities continue to alter the global nitrogen cycle, the ability to predict the impact of increased nitrogen loading to freshwater systems is becoming more and more important. Nitrogen retention is of particular interest because it is through its combined processes (denitrification, nitrogen sedimentation and uptake by aquatic plants) that local and downstream nitrogen concentrations are reduced. Here, we compare the magnitude of nitrogen retention and its components in wetlands, lakes and rivers. We show that wetlands retain the highest proportion of total nitrogen loading, followed by lakes and then rivers. The differences in the proportion of N retained among systems is explained almost entirely by differences in water discharge. Denitrification is the primary mechanism of nitrogen retention, followed by nitrogen sedimentation and uptake by aquatic plants.