The development of wastewater treatment systems, including competitive methods for nitrogen and phosphorus removal, is focused on intensifying final technological effects with due care taken for economic and environmental concerns. Given the possibility of integrating wastewater treatment processes with biofuel production, the prospective seems to be technologies harnessing microalgal biomass. The present study aimed to verify the feasibility of applying T. subcordiformis genus microalgae as the third stage of the dairy wastewater treatment process and to determine microalgae biomass production effectiveness and hydrogen yield in the biophotolysis process. The study proved that microalgae cultivation with dairy wastewater was nearly 35% less effective compared to that with a chemically pure medium. Nitrogen and phosphorus compounds contaminating wastewater were found to represent an available source of nutrients for T. subcordiformis population. The volume of hydrogen produced ranged from 116 ± 7 cm3 to 162 ± 7 cm3, and the percentage of H2 content in the biogas ranged from 55.4 ± 2.2% to 57.2 ± 4.1%. A significantly higher hydrogen yield per initial biomass concentration, reaching 69 ± 4.2 cm3/go.d.m., was determined in the variant with wastewater accounting for 50% of the culture medium. The respective value noted in the control respirometer was 54 ± 2.1 cm3/go.d.m.