Human alteration of the nitrogen cycle has led to increased riverine nitrogen loads, contributing to the eutrophication of lakes, streams, estuaries, and near-coastal oceans. These riverine nitrogen loads are usually less than the total nitrogen inputs to the system, indicating nitrogen removal during transport through the drainage network. A two-year monitoring study quantified the ammonium, nitrate, and organic-N inputs, outputs, and inferred in-stream processes responsible for nitrogen transformations and removal in a 1900 m reach of a drainage canal located in a managed pine plantation. Total nitrogen inputs to the canal section were 527.8 kg in 2001 and 1422.7 kg in 2002. Total nitrogen discharge at the outlet was 502 kg in 2001 and 1458 kg in 2002. The mass balance of nitrogen inputs and outputs indicated a loss of 25.8 kg (5.1%) of total nitrogen from the system in 2001, and a gain of 35.3 kg (2.4%) of total nitrogen to the system in 2002. Variability in the input and output estimates was high, especially for groundwater exchange. Different hydrologic and nitrogen inputs and outputs were identified and quantified, but measurement variability obscured any potential nitrogen removal from the system.