Cyanobacteria are capable of rapidly sequestering CO2 into lipid-enriched biomass while utilizing dissolved inorganic nutrients in wastewater. Semi-batch 30-d cultures of Anabaena sphaerica and A. variabilis were simultaneously monitored for biomass and lipid productivities, CO2 sequestration rates and dissolved macronutrient (N, P) utilization rates under varying photoperiods (8, 10, 12, 14, 16 and 18 h) and CO2 concentrations (control (air), 2% and 5%) in media supplemented with 15% (v/v) agricultural run-off water in bubble column photobioreactors. Effect of enhanced CO2 supply was significantly beneficial for all parameters. Longer or shorter photoperiods from the originally acclimated 14 h led to diminished and enhanced parameters respectively, but these changes were staggered due to inherent adaptibilities. The long-chain fatty acid (LCFA) profiles of A. sphaerica and A. variabilis were respectively dominated by saturated fatty acids (SFA) and polyunsaturated fatty acids (PUFA). Eight LCFAs were common between the two species while the SFA myristic acid was found in A. sphaerica and the ω-6 PUFA cis-8,11,14-eicosatrienoic acid was found in A. variabilis. It was concluded that A. sphaerica and A. variabilis showed potential in biodiesel and nutraceutical production, respectively. However, culture conditions including photoperiod and CO2 supply were found to affect the LCFA profiles slightly. © 2019 Elsevier B.V.