The current research was carried out to evaluate the impact of treating wheat (Triticum aestivum c.v Sakha 93) seeds and irrigation water magnetically in combination with different sources and rates of nitrogen on wheat productivity and grain quality under saline soil conditions. Two feld experiments were carried out during the winter seasons 2018–2019 and 2019–2020 in a split split randomized complete block design with four replicates at ElRabaa village, Bir Al-Abd, North Sinai Governorate, Egypt. Main plots were assigned to N-sources, urea, and compost; sub-plots were N-rates 0, 119, 179, and 238 Mg N ha−1, while magnetic treatment of irrigation water and wheat grains was in sub-subplots. The highest chlorophyll and carbohydrate contents (3.12 mg g−1 f.w. and 783 g kg−1, respectively) were observed due to compost, N4+ (MS + MW) treatment representing an increasing percentage of 189% and 220%, respectively. The maximum plant height, spike length, No. spike plant−1, and spike weight values were 82.0 cm, 15.1 cm, 13.9, and 24.9 g plant−1. The results were due to the addition of compost at a rate of 238 kg N ha−1 in combination with magnetized seeds and water treatment with 224, 643, 546, and 845% over the untreated treatment. The maximum straw and grain yields (11.7 and 7.29 Mg ha−1, respectively) were achieved due to the application of compost at a rate of N3 + (MS + MW), and the corresponding increments over the non-treatment plants were 718 and 846%, respectively. However, treatment of compost (179 Mg N ha−1 + magnetized seeds and water) resulted in the maximum increases in the No. grains spike−1, grains weight, 1000-grains weight, protein content, N, P, K, Fe, Mn, and Zn-uptake by grains. Soil pH and EC values were decreased, especially for plants treated with compost (238 kg N ha−1 + magnetized seeds and water treatment).