Zonal geranium (Pelargonium × hortorum ‘Real Mintaka’) and petunias (Petunia × hybrid Hort. Vilm.-Andr. ‘Giove’) were grown in closed soilless systems to evaluate the effects of irrigation system (drip and subirrigation) and nutrient solution concentration (half and full) during spring growing season in terms of substrate electrical conductivity (EC(s)), growth, quality, crop evapotranspiration, and growth index water use efficiency (WUE(GI)). For both crops, at the end of the cultural cycle the highest EC(s) in the upper and lower layers were recorded in plants fertilized with the full strength solution, whereas the effect of irrigation system was less pronounced where the highest EC(s) was recorded in subirrigation but only in the upper layer. The highest EC(s) recorded with subirrigation under full strength nutrient solution on geranium had a negative effect on plant growth parameters (shoot dry weight, root-to-shoot ratio, final leaf area, and growth index) and on number of flowers, while no significant effects were observed for petunia, indicating that this bedding plant can be considered more tolerant to salinity. No significant differences among treatments were recorded for the petunia WUE(GI), whereas for geranium the lowest value of WUE(GI) was observed in the subirrigation treatment using half strength nutrient solution.