Hydrogen (H2) production using a biological pathway such as anaerobic digestion suffers limitations in the survival of microorganisms. Usually, microalgae are used as feedstock but the acidic pH of digestate ruptures the cell wall of microalgae resulting in dead cellular debris. Whereas some cyanobacteria (blue-green microalgae) are very resilient and tolerant to stressful environments such as hypersaline conditions. Therefore, in this study, a microbial consortium (co-culture) of cyanobacteria Phormidium keutzingianum and activated sludge bacteria (ASB) was established to generate H2 production from waste resources. Different co-culturing ratios 2:1, 1:1, and 1:2 v/v (P. keutzingianum: ASB) were analyzed for H2 production with glucose, sorbitol, and mannitol as carbon substrates. In addition, the effect of different concentrations (0, 10, and 20 g/L) of salt (NaCl) on H2 production was also tested. Results indicated that the amount of cumulative H2 produced changed significantly by varying the carbon substrates. Glucose-supplemented co-culture produced the lowest amount of H2 at 278 mL/L as compared to 980 and 562 mL H2/L in sorbitol and mannitol-supplemented co-cultures, respectively. The addition of NaCl negatively affected H2 production by increasing the salinity level from 0 to 20 g/L, and the cumulative H2 reduced from 980 to 176.8 mL/L and 562 to 333 mL/L in sorbitol and mannitol-supplemented co-culture, respectively. Sorbitol showed cyanobacterial growth in terms of chlorophyll from 600 to 1200 μg/L and optical density from 1 to 12 at λ 620 nm. Total organic carbon (TOC) in sorbitol supplemented co-cultures also increased to the peak 5.7, 6.7, and 7.7 g/L in 2:1, 1:2, and 1:1 v/v ratios, respectively, indicating anaerobic growth. Hence, this study signifies that sorbitol appeared to be the significant carbon substrate that helped cyanobacteria grow under anaerobic conditions resulting in higher H2 production. Moreover, cyanobacteria are more tolerant to stressful environments such as hypersaline and acidic conditions compared to microalgae.