Magnetic or oxidation treatment of irrigation water can promote the transport of water and nutrients by the root system, improve the efficiency of water and fertilizer use and potentially increase yields. Hydroponic and field experiments were conducted to explore how irrigation with magnetized and/or oxidized water affects grain yield and water-use efficiency (WUE) in winter wheat with an emphasis on physiological changes in the root system. Hydroponic cultivation of winter wheat with pure groundwater and brackish water included the following treatments: control group (CK−G, CK−B); magnetization (GM, BM); oxidation (GO, BO); and the combination of magnetization and oxidation (G(M+O), B(M+O), G(O+M), B(O+M)). Field experiments only tested irrigation with various types of groundwater, including the control group (IG), magnetization treatment (IGM), oxidation treatment (IGO), and the combination of the two treatment methods (IG(M+O), IG(O+M)). Hydroponic cultivation revealed that the magnetic treatment and oxidation of both groundwater and brackish water can significantly improve the root vigor of winter wheat, i.e., improvements of 100.5–253.7% and 100.4–213.9% were seen in the groundwater and brackish treatment groups, respectively, relative to the control group. The root length density (RLD) of wheat increased by 67.6% (GM), 79.4% (GO), 7.5% (BM), and 40.0% (BO) relative to the respective control groups (CK−G and CK−B). Moreover, the root weight density (RWD) for BO and B(O+M) treatments improved significantly (66.7% and 55.4%, respectively) relative to CK−B. The maximal increases in root surface area density (RSD) were observed in treatments GO and B(O+M), which showed values 125% and 100%, respectively, higher than what was measured for the control groups. The root/shoot ratios of the GO and G(O+M) treatments improved significantly (by 75.3% and 62.0%, respectively) relative to CK−G. The results of field experiments showed that wheat in the IGO and IG(O+M) plots absorbed more water from the soil than wheat in the of IG plots (increases of 13.9% and 16.9%, respectively). Furthermore, the IGO and IG(O+M) treatments produced significantly higher grain yields and WUE than the IG plots, with IGO producing the maximum yield (11.7 × 103 kg ha−1) and IG(O+M) the highest observed WUE (30.3 kg ha−1 mm−1). Hence, the research provides clear evidence that the irrigation of winter wheat with magnetized and/or oxidized water can increase grain yields and WUE.