Textile wastewater (TW) contains toxic pollutants that pose both environmental and human health risks. Reportedly, some of these pollutants, including NO3-, NO2- and reactive black 5 (RB-5) dye, can be removed via hydrogen-based denitrification (HD); however, it is still unclear how different factors affect their simultaneous removal. This study aimed to investigate the effect of H2 flow rate, the sparging cycle of air and H2, and initial dye concentration on the TW treatment process. Thus, two reactors, an anaerobic HD reactor and a combined aerobic/anaerobic HD reactor, were used to investigate the treatment performance. The results obtained that increasing the H2 flow rate in the anaerobic HD reactor increased nitrogen removal and decolorization removal rates. Further, increasing the time for anaerobic treatment significantly enhanced the pollutant removal rate in the combined reactor. Furthermore, an increase in initial dye concentration resulted in lower nitrogen removal rates. Additionally, some of the dye was decolorized during the HD process via bacterial degradation, and increasing the initial dye concentration resulted in a decrease in the decolorization rate. Bacterial communities, including Xanthomonadaceae, Rhodocyclaceae, and Thauera spp., are presented as the microbial species that play a key role in the mechanisms related to nitrogen removal and RB-5 decolorization under both HD conditions. However, both reactors showed similar treatment efficiencies; hence, based on these results, the use of a combined aerobic/anaerobic HD system should be used to reduce organic/inorganic pollutant contents in real textile wastewater before discharging is recommended.