To compare the effect of magnetic drip irrigation and conventional irrigation with different salinity levels on water productivity and yield of sunflower (Helianthus annuus L.), a factorial experiment was conducted using a completely randomized design with 6 treatments and 3 replicates at the Research Station of the Faculty of Water Sciences Engineering, Shahid Chamran University of Ahvaz, Iran. The experiment was executed over the crop year 2018–19. The treatment variables consisted of 2 types of water (magnetically treated and non-magnetically treated) and 3 salinity levels (Karun River water (S1), 4 dS/m (S2), and 6 dS/m (S3)). The use of magnetically treated irrigation water increased the biomass water use efficiency, and the weight of 100 seeds by 13.9%, and 5.48%, respectively. With the conventional irrigation method, increased salinity reduced the seed yield. The highest seed yield and irrigation water productivity were observed at 4 459 kg/ha and 0.73 kg/m3 for grain yield at a water salinity level of S1 (the control treatment). The application of water with salinity of 4 dS/m and 6 dS/m (S2 and S3) caused a reduction in seed yield by 9.3 and 21.8%, respectively, in comparison to that of the control treatment. Moreover, irrigation water productivity for the biomass yield decreased by 14.57 and 29.23%, respectively. Based on the results of this study, the use of magnetically treated water can reduce the effects of salinity stress under conditions of salt stress. Therefore, magnetically treated water can increase the yield and productivity of irrigation water.