Disposal of salinized drainage water is a problem in the irrigated San Joaquin Valley of California and it has been proposed that this water could be used judiciously in the culture of wheat Triticum aestivum L.). This may require breeding of cultivars specifically for this cropping system and the effects of saline irrigation on end‐use quality may be affected. These considerations were addressed in a field study where salinity concentration of irrigation water was controlled and water uniformly applied over test plots. Two agronomically desirable cultivars, Anza and Cajeme 71, and 43 random recombinant inbred lines derived from their hybrid were studied for two successive years with two N fertilization levels and three salinity levels. Nitrogen effects were minimal in this study because of a high level of basal N in the experimental site. Wheat flour quality and baking performance were improved by saline irrigation in the first year, but in the second year, when grain filling was poor, quality was adversely affected by salinity. High‐molecular‐weight glutenin alleles from Cajeme 71 at the Glu‐l locus were associated additively with improved flour protein content (Glu‐Al, Glu‐Dl), breadloaf volume (Glu‐Bl), and SDS sedimentation (Glu‐Dl). There was little or no interaction of the Glu‐l alleles with salinity for flour protein content and mixing time. Only one epistatic interaction effect out of 80 tested was significant (αABD for bake water absorption at high salinity in 1986). The additive effects were generally similar at the two salinity levels although interactions were detected which were less than 10% of the phcnorypic variance.