To reduce nitrate contamination of groundwater in intensive agricultural production areas, crop producers should identify nitrogen (N) inputs and outputs to calculate potential N available for leaching into groundwater. However, poor understanding of N fate in container plant production may result in inaccurate estimation of potentially leachable N. To improve understanding of container-applied N fate, an experiment was conducted to measure N inputs and outputs from a woody ornamental plant (Lagerstroemia indica ‘Whitt II’) production system fertilized with controlled-release and surface-applied fertilizer. Two experimental bed types, polyethylene-lined and unlined, were installed at a production nursery in California. Measured N inputs included: the substrate, with fertilizer and roots, and irrigation water N. Outputs included: N remaining in the substrate and plant shoots at the end of the production cycle, nitrous oxide-N gas lost from the substrate and bed soil, and aqueous N lost in runoff during the production cycle. There was a significant difference in runoff N losses from the lined and unlined beds. The difference in runoff N lost between bed types was the amount of N infiltrating into the soil below the growing bed surface. The majority of input N either remained in the growing substrate (57%) at end of production cycle or was taken up by the plant shoots (5%). Nitrous oxide-N lost from the growing substrate and the bed soil was 1.5% and 0.01% of input N, respectively. Runoff and soil infiltration N accounted for 6.5% and 2.4% of input N, respectively. Unaccounted N was 27.7% of input N and is attributed to complete denitrification. Future work should address the amount of aqueous N lost from the growing substrate to reduce surface and groundwater contamination.