Knowledge of carbon (C) and nitrogen (N) dynamics under different irrigation practices in pomegranate orchards is novel and essential to develop sustainable production systems. The aim of this research was to determine the effect of high-frequency drip irrigation and different rates of N fertilizer on C and N distribution in the soil and N uptake by pomegranate fruit and leaves. The main treatments were surface drip irrigation (DI) and subsurface drip irrigation (SDI), and the sub-treatments used were three initial N rates (N1, N2, and N3). As trees grew larger, the N application rate increased. From 2013-2015, trees received the following rates of N: 62-113 (N1), 166-263 (N2), or 244-342 kg/ha (N3). Soil and leaf total C (TC) and N (TN), soil dissolved organic C (DOC), soil nitrate (NO 3 − ), and total N uptake by fruit were evaluated between 2012 and 2015. Soil samples were collected to 120 cm depth at 15 cm increments. DI resulted in higher concentrations of TN, TC, NO 3 − , and DOC in the upper 75 cm depth than SDI. The N3 treatment resulted in higher concentrations of TN, TC, NO 3 − , and DOC under both DI and SDI. Neither DI nor SDI at the N1 or N2 levels increased TN and NO 3 − concentrations at 105-120 cm soil depth, indicating reduced leaching risk using high-frequency drip irrigation. Higher N uptake by fruit was observed in SDI than in DI in 2014 and 2015, and in N2 and N3 treatments compared with N1 in 2013 and 2014. The data indicate that the application rate at 166-263 kg/ha (N2) provided sufficient N for a 4-6-year-old pomegranate orchard and that high-frequency SDI is a promising technology for achieving higher N use efficiency and minimizing leaching loss of NO 3 − and DOC.