We evaluated the performance and determined the efficiency parameters of an automated subirrigation system in a commercial greenhouse facility for clonal eucalyptus (Eucalyptus sp.) seedling production to improve subirrigation management practices. A methodology based on the mass balance of the irrigation system was established to determine the volumes of nutrient solution (NS) applied, drained, stored, evapotranspirated, and leaked in each subirrigation bench. The application, drainage, and NS dwell time in the 55-cm3 conic containers (0.125 m height × 0.03 m diameter) and the depth of NS reached inside the bench were also assessed. The values of application efficiency, irrigation efficiency and system transport (supply and drainage), and disposal losses of NS were estimated for each bench and inferred for the entire subirrigation system. The benches had average application and irrigation efficiency values of 0.84% and 98.38%, respectively. The system showed irrigation efficiency values of 27.59% and the sum lost by transport, leakings, and disposal in the water treatment plant of 72.41%. The continuous return of NS because of the high irrigation frequency contributed to this loss, resulting in 10,070 L of NS consumed by the plants and 26,430 L lost after 15 days of cultivation. Our results demonstrated that the system presented an adequate irrigation efficiency, but a low application efficiency caused by the constant return of NS because of the high irrigation frequency and the excess of losses from leaking and disposal of NS after 15 days of cultivation. Nevertheless, the system operated like a hydroponic system, which kept the containers partially immersed in the NS and did not use the full substrate container capacity to provide adequate moisture. This reduced the overall system irrigation and the substrate storage efficiencies, which needs to be improved by proper equipment design, operation, water and nutrients use efficiency, and management to achieve all the benefits that subirrigation possess.