Agriculture, due to a growing scarcity of fresh water resources, often uses low-quality waters for irrigation, such as saline waters. However, unmanaged applications of such waters may have negative environmental and economic consequences. Based on the concept of the water footprint (WF), a measure of the consumptive and degradative water use, the field-calibrated and validated HYDRUS (2D/3D) model was applied to find optimal management scenarios (from 1980 different evaluated scenarios). These scenarios were defined as a combination of different salinity rates (SR), irrigation levels (IL, the ratio of an actual irrigation water deth and a full irrigation water depth), nitrogen fertilization rates (NR), and two water-saving irrigation strategies, deficit irrigation (DI) and partial root-zone drying (PRD). The consumptive WF was defined as the crop water consumption divided by the crop yield. The grey WF was calculated for the N fertilizer and defined as the volume of freshwater required to dilute nitrogen (N) in recharge so as to meet ambient water quality standards. Simulated components of water and solute dynamics were used to calculate criteria indices, which were divided into two groups: (a) environmental indices, including the degradative grey water footprint (GWF) and the apparent N recovery rate efficiency (ARE), and (b) economic indices, including economic water (EWP) and land (ELP) productivities. While significant improvements of 3.9–59.2%, 0.1–165.8%, and 0.01–166.5% in ARE, EWP, and ELP, respectively, were obtained when NR varied within the range of 0–200 kg ha−1, changes in these indices were relatively minor when NR was higher than 200 kg ha−1. At a given NR, GWF tends to increase considerably by up to 180% when DI-crops are subject to low-intermediate salt (SR < 7 dS m−1) and water (IL > 70%) stresses. This is at the expense of up to a 55% reduction in ELP and up to a 120% increase in EWP. With N uptake 0.2–17.3% higher, PRD seems to be a more viable agro-hydrological option than DI in reducing a pollutant load into regional aquifers as well as in sustaining farm economics. The entire analysis reveals that the PRD strategy with N-fertilization rates of 100-200 kg ha−1, a moderate salinity stress (SR < 5 dS m−1), and irrigation levels of 60–90% represents the best management scenario. It can be concluded that, while there is a substantial need for rescheduling irrigation and fertilization managements when crops are irrigated with saline waters, HYDRUS modeling may be a reliable alternative to extensive field investigations when determining the optimal agricultural management practices.