Abstract Hydrogen production by Nostoc linckia was studied using both free and alginate immobilized biomass of the cyanobacterium in separate lab-scale photobioreactors (PBRs). Hydrogen production rates improved significantly when immobilized cyanobacterial biomass was used in PBR and the production continued up to 25 days by maintaining required anoxic conditions and carbohydrate supplement. Average hydrogen production rate over 25 days was 132 μmolH 2 /h/mg Chl a. The biological waste from the PBRs was utilized for sequestration of two toxic heavy metals (chromium and cobalt) and carcinogenic dyes (Reactive Red 198 and Crystal Violet) from aqueous solutions in packed-bed column. From the PBR containing free N. linckia cells, the spent biomass was collected after 7 d, dried and immobilized in alginate matrix, and used as a biosorbent for optimizing bed height and flow rate of the column. Breakthrough capacity of the packed-bed column was determined and breakthrough curves were analyzed using BDST model. Three PBRs containing immobilized cyanobacterial biomass were run for 5, 15 and 25 days, and the biological waste collected at the end of the operation was used for biosorption studies under optimized conditions (bed height, 25 cm; flow rate, 3 mL/min). Biosorption efficiency of the waste biomass was found to be influenced by the operation time of the hydrogen photobioreactor.