In citrus production, the combination of adequate irrigation and nitrogen (N) management is considered a key factor in improving N uptake efficiency, so as to minimize nitrate ( ) leaching below the root zone and maintain optimal crop yield. The response of eight-year-old citrus trees grown in lysimeters to two combinations of fertilizer and water management techniques – split N application in drip irrigation (DI-F) vs. a single broadcast application with flood irrigation (FI-B) – was compared by means of the use of a ¹⁵N-labeled fertilizer (ammonium nitrate). Soil sampling 54, 116, 175 and 238 days after the beginning of the experiment and destructive harvest of trees at the end of the growing cycle allowed the determination of the fate of the labeled fertilizer supplied. The ¹⁵N recovered in the different compartments of the plant-soil system and fertilizer nitrogen uptake efficiency (FNUE, ¹⁵N taken up by the plant per ¹⁵N supplied) was also quantified. Irrigation-fertilizer management practices had no effect on either total tree biomass or in fruit yield; however, a significantly greater development of coarse roots in the DI-F treatment was recorded. Fertilizer-N uptake was 25% higher in trees in the DI-F than in the FI-B treatment; fine roots and fruits of DI-F trees accumulated 2.1- and 1.4-fold higher fertilizer-N, respectively, compared to the corresponding organs of FI-B trees. At the end of the experiment, -¹⁵N concentrations in the 0–20 cm and 60–90 cm layers of DI-F trees were higher than those in FI-B trees, whereas no differences were recorded for -¹⁵N concentrations of both treatments. Potential nitrate leaching (PNL) 54 days after the beginning of the experiment represented 8% of fertilizer-¹⁵N delivered in FI-B, whereas in DI-F it was almost negligible. In DI-F trees, PNL become noticeable on day 175, highlighting the effect of this irrigation method in reducing and slowing down the movement through the soil profile. At the end of the experiment PNL represented 14% and 5% of fertilizer supplied for FI-B and DI-F, respectively. FNUE was significantly higher (12%) with the DI-F treatment when compared to FI-B treated trees. Comparison of the two water-fertilizer management practices studied in the present work allowed us to conclude that the DI-F treatment increased FNUE while diminishing nitrate leaching, when compared to the FI-B treatment.