Abstract Egypt's irrigation systems are inefficient; the use of water is profligate and soil salinity levels have risen. This has reduced agricultural yields and biased production patterns away from high value crops in favour of salt resistant crops. The need to improve irrigation water quality is accentuated by increasing demand for, and declining supplies of, water resources. This study uses a Computable General Equilibrium model, calibrated to an extended SAM and detailed satellite accounts for water quality, to assess the impacts of the huge investments needed to raise water quality. The results indicate strong positive economy-wide impacts in Egypt, which exceed the investment cost. Income increases by 4% and induce increases in the production of high-value crops; i.e., fruits (almost triple), seasonal vegetables (30–37%) and rice by (13%) with a 64% increase in rice exports. The study illustrates the importance of including water quality as a variable in the analyses of water systems.