Biochar application is a promising sustainable strategy for enhancing soil properties thus crop production. However, biochar application to soil certainly alters its biological and physical properties, and could require extra costs. Therefore, biochar suitability to agroecosystems must be proactively estimated. The advantage of biochar addition to poor fertile or weathered soils has been well studies, however, its feasibility to fertile soil under low quality (saline) irrigation water was not frequently studied. Consequently, this work investigates the hypothesis of whether the application of biochar at a rate of 4.8 tons/ha to fertile soil (Nile Valley, Giza, Egypt) would ameliorate the negative effects of saline irrigation regime (3000 ppm) on tomato crop and soil. The results of two seasons experiments showed that saline irrigation significantly reduced tomato crop yield by an average reduction ratio of 51%, and biochar addition could not compensate such reduction. Furthermore, biochar did not reduce accumulated Na+ in fruits or roots. Tomato fruits produced from biochar-added soil were lower in TSS levels (41.7% reduction ratio) yet larger in diameter by approximately 1.5-fold increase. Interestingly, biochar addition into soil greatly promotes the length of stem-borne lateral roots and elevates the expression of LeNR (encodes nitrate reductase enzyme) in leaves yet under fresh irrigation regime. For soil properties, biochar application enhanced the soil properties under either saline or fresh water irrigation conditions. Collectively, it is assumed that biochar application to fertile soil in Nile Valley of Egypt could not alleviate tomato fruits yield reduction affected by applied saline irrigation regime.