The development and implementation of innovative production technologies have a direct influence on the creation of new sources of pollution and types of waste. An example of this is the wastewater from soil-less agriculture and the effluent from microbial fuel cells. An important topic is the development and application of methods for their neutralisation that take into account the assumptions of global environmental policy. The aim of the present study was to determine the possibilities of utilising this type of pollution in the process of autotrophic cultivation of the biohydrogen-producing microalgae Tetraselmis subcordiformis. The highest biomass concentration of 3030 ± 183 mgVS/L and 67.9 ± 3.5 mg chl-a/L was observed when the culture medium was wastewater from soil-less agriculture. The growth rate in the logarithmic growth phase was 270 ± 16 mgVS/L-day and 5.95 ± 0.24 mg chl-a/L-day. In the same scenario, the highest total H2 production of 161 ± 8 mL was also achieved, with an observed H2 production rate of 4.67 ± 0.23 mL/h. Significantly lower effects in terms of biomass production of T. subcordiformis and H2 yield were observed when fermented dairy wastewater from the anode chamber of the microbial fuel cell was added to the culture medium.