Soilless culture is considered the mostpromising, intensive, and sustainable approach with various advantages for plant production in terms of saving water and nutrients. It can provide consumers with sufficient and high-quality food. However, the commonly used growing substrate for soilless cultivation, coconut fiber (CF), is usually imported and expensive or even unavailable. The objectives of this study were to investigate the impact of local organic farm resources substrates on tomato (Solanum lycopersicum L.) plant growth, water relations, photosynthesis, chlorophyll fluorescence, and phytochemical analysis of fruits in a hydroponics culture system. Two growth substrates were evaluated: date-palm waste composted with animal manure (7:3 w/w) (DPAM) and date-palm trunk compost (DPT). CF and local soil were utilized as positive and negative controls, respectively, in randomized blocks. The results revealed that DPAM substrate enhanced plant growth and physiology: shoot development, leaves tissues hydration, and photosynthetic parameters, as well as chlorophyll fluorescence. However, DPT and CF improved fruit quality: water, mineral, sugar, and protein content. The antioxidant activity of the fruit extract was the greater in DPAM, reaching 13.8 mg GAEg−1 DW. This value wasdecreased in soil by 40%. Photosynthesis activity was the most important in DPAM with 12 µmol CO2 m−2 s−1, and only 6.4 µmol CO2 m−2 s−1 in the soil condition. However, regarding the non-photochemical quenching, the dissipated light energy was greater in soil (0.096 ± 0.02) than in DPAM (0.025 ± 0.04). Date-palm waste-based substrates improved tomato vegetative growth and fruit quality as compared to soil-based culture. Date-palm waste-based substrates supplemented with manure appear to be promising and less expensive alternatives to the coconut fiber substrate extensively used in soilless crops in North Africa.