The Central Valley Regional Water Quality Control Board required agricultural producers to document nitrogen (N) inputs and outputs to complete Irrigation and Nitrogen Management Plans (INMP) for estimation of potentially leachable N. A system nitrogen balance was developed to reduce uncertainty in output N from soilless substrate-based production systems. 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 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. Environmentally harmful discharges were identified as aqueous N and nitrous oxide (N2O) lost from the substrate. Very little research has been conducted to understand N2O emissions from soilless substrates. A Douglas fir (Pseudotsuga menziesii) bark-based substrate planted with Crepe Myrtle (Lagerstroemia indica ‘Whitt II’) had controlled release fertilizer incorporated with differing amounts of surface-applied fertilizer. Gas flux and pour-through extract samples were regularly collected. A regression model indicated that significant predictors of N2O flux were pour-through extract ammonium and nitrate concentration, volumetric water content, and substrate temperature. The total California-scaled fir bark-based substrate production system N2O-N emissions were greater than for soil-grown California horticultural crops. Nitrous oxide emissions from soilless substrates are believed to be from heterotrophic denitrification but soilless substrates have physical and chemical properties that could promote nitrification- and denitrification-derived N2O simultaneously. Fir bark, peat, and peat:fir bark substrates were fertilized with 15NH4NO3, NH415NO3, unenriched NH4NO3, or unfertilized to determine contribution of nitrification and denitrification to N2O production in soilless substrates. Heterotrophic denitrification accounted for almost all the N2O emitted from all three substrates but played a larger role in the fir bark and peat:fir bark substrates. Nitrification-derived N2O emissions began on day 11 in the peat substrate and continued to increase until the experiment ended, contributing to 6% of total N2O emission from this substrate. Fundamental research to understand N2O emissions from soilless substrates must be conducted to develop best management practices to reduce global warming potential from soilless-substrate production systems.