World recent concerns about the shortage of water resources and contamination of groundwater supplies have motivated scientists seeking for more efficient techniques in irrigation and fertilization of farms while taking the advantage of models. The objective of this study is to address how water and nitrogen (N) dynamics are affected by efficient management strategies and to evaluate the application of HYDRUS-1D model in these conditions. In terms of using management policies, different irrigation strategies, planting methods, and different N fertilization rates applied on safflower (Carthamus tinctorius L.) in volumetric field lysimeters. The irrigation regimes were ordinary furrow irrigation (OFI) and variable alternate furrow irrigation (VAFI) as a partial root drying (PRD) technique. The planting methods were on-ridge planting (P1) and in-furrow planting (P2) methods. The fertilizer levels were 0 (N0), 100 (N1), and 200 (N2) kg ha of urea as 0, 46, and 92 kg N ha. Results showed that VAFI regime and in-furrow planting method favorably reduced the amount of drainage water below safflower root zone in comparison with the ordinary methods. Furthermore, VAFI regime satisfactorily decreased the seasonal nitrate (NO-N) leaching below the root zone, whereas differences between the leached NO-N in in-furrow and on-ridge planting methods were not significant. Moreover, VAFI regime did not show any negative effects on total N uptake in safflower seed and straw, whereas in-furrow planting accumulated higher N in comparison with the on-ridge planting method. In addition, safflower nitrogen (N) uptake was responsive to application of nitrogen, although the rate of increase in N accumulation was not significant between the application rates of 46 and 92 kg N ha. The soil nitrate concentration decreased during the growing season indicating that safflower root system has a great ability in absorption of NO-N from soil N supplies. HYDRUS-1D model favorably predicted the drainage water, nitrate concentration of drainage water, crop N uptake, and residual soil NO-N concentration for safflower field. Therefore, it can be an applicable model for prediction of water and nitrogen dynamics, despite of two-dimensional flow conditions in furrow irrigation. It was concluded that VAFI strategy and in-furrow planting method are suitable alternatives helping farmers produce food while conserving water and preserving the environment.