Irrigated agricultural lands in arid regions often suffer from soil salinization and lack of drainage, which affect environmental quality and productivity. Integrated Farm Drainage Management (IFDM) systems, where drainage water generated from higher‐valued crops grown on high quality soils are used to irrigate salt‐tolerant crops grown on marginal soils, is one possible strategy for managing salinity and drainage problems. If the IFDM crop were a biofuel crop, both environmental and private benefits may be generated; however, little is known about this possibility. As such, we develop a bioeconomic programming model of irrigated agricultural production to examine the role salt‐tolerant biofuel crops might play within an IFDM system. Our results, generated by optimizing profits over land, water, and crop choice decisions subject to resource constraints, suggest that based on the private profits alone, biofuel crops can be a competitive alternative to the common practices of land retirement and nonbiofuel crop production under both low to high drainage water salinity. Yet IFDM biofuel crop production generates 30–35% fewer GHG emissions than the other strategies. The private market competitiveness coupled with the public good benefits may justify policy changes encouraging the growth of IFDM biofuel crops in arid agricultural areas globally.