Shortage and salinity of irrigation water are two major constraints that influence wheat production in arid and semi-arid regions of Iran. In this study, effects of deficit furrow irrigation with different salinity levels and planting methods (in-furrow and on-ridge) as strategies for coping with water and salinity stress on yield and yield quality of winter wheat was investigated in a two-year experiment. Irrigation treatments were full irrigation (FI), 0.65FI, and 0.35FI, and salinity levels of irrigation water were 0.6 (well water), 5.0, 7.5, and 10.0 dS m−1. In the first year, grain yield was reduced by 20% and 26% in irrigation regimes of 0.65FI (381 mm) and 0.35FI (217 mm), respectively. These reductions were 17% and 30% in the second year, respectively. The corresponding irrigation water reductions were 33% and 62% in both years for 0.65FI (381, and 355 mm compared to 573 mm) and 0.35FI (217, and 203 mm compared to 533 mm), respectively. Therefore, it is indicated that the proportion of irrigation water reduction to the grain yield reduction is 2:1 in benefit of the deficit irrigation mostly due to the seasonal rainfall of 363 and 439 mm in the first and second years, respectively. Although the majority of rainfall occurred in winter, the winter wheat growth is at rest. Results also indicated that in FI with irrigation application efficiency of 80% (leaching fraction of 20%), the salinity level of 3.36 dS m−1 produced no grain yield reduction. Furthermore, salinity level of 7.5 dS m−1 for irrigation regimes of 0.65FI and 0.35FI, respectively did not show significant difference in grain yield compared with that obtained in 0.6 dS m−1 salinity level. Therefore, by deficit irrigation, higher salinity level is applicable due to lower salt accumulation in soil. In-furrow planting resulted in 4% (statistically significant) higher grain yield compared with that obtained in on-ridge planting with 5% higher irrigation water productivity (IWP). By considering acceptable grain yield production in 0.65FI, its IWP (1.03 kg m−3 and 1.1 kg m−3 in the first and second year, respectively) was significantly higher than those obtained in FI (0.85 kg m−3 and 0.87 kg m−3 in the first and second year, respectively). In in-furrow planting, grain yield in salinity level of 7.5 dS m−1 was suitable with irrigation regime of 0.65FI; whereas, for on-ridge planting appropriate salinity is 5.0 dS m−1. Therefore, in non-limited irrigation water condition, FI with salinity level of 5.0 dS m−1 and in-furrow planting is the appropriate irrigation management for winter wheat. However, with limited water supply, 0.65FI with salinity of 7.5 dS m−1 and in-furrow planting would be appropriate in winter wheat irrigation management in the study region. The root water uptake was predicted by Homaee-Feddes method with higher accuracy and its value was used in grain yield prediction with Doorenbos-Kassam yield-ET function with higher accuracy.