To mitigate Nitrous Oxide (N2O) emissions derived from Nitrogen (N) fertilizer of agroecosystems, establishment of best management protocols for cultivation is necessary. Hydroponic systems using rockwool have the potential to reduce N2O emissions; however, the effects of nutrient condition and retained N compounds in rockwool on N2O emissions remain unclear. The primary objective of our study was to understand the crucial factors behind emissions of N2O. Tomato cultivation with low levels of nutrient showed reduced growth and yield, but increased N2O emission. In contrast, growth and N2O emissions were increased by cultivation with normal levels of nutrient and used (1-yold) rockwool containing excess N compounds from the previous year's cultivation.