Abstract Major challenges in cultivation, harvesting, CO2 capture and downstream processing of microalgae biomass have to be confronted for successful commercial deployment. This study explored a sustainable process train to mass-produce a native marine algal strain, Nannochloropsis salina, for biocrude production and CO2 capture. The microalga was cultivated in a 3-m2 raceway pond with manual agitation, 10-m2 raceway ponds with and without CO2 supplementation and a 120-m2 pond with CO2 supplementation using carbonation column reactor (CCR). During the above experiments, the areal productivities obtained ranged from 7.5 to 34.4 g m−2 d−1 and the lipid content was between 29 and 80%. This study also demonstrated a novel 10 KLPD (kilolitres per day) capacity electropreciflocculation (ePF) reactor (∼0.56–0.78 KWh/KL) and filter press for biomass harvesting with 98.24% efficiency. The CO2 capture of N. Salina estimated was in the range of 45.38–208.12 tons ha−1 y−1, and the average was 95.39 tons ha−1 y−1. The cost estimated based on the 120-m2 pond trials was $3.46/kg of dry algal biomass. Thus the findings provide immense scope for future research on large-scale cultivation of Nannochloropsis salina for biofuel production and carbon capture applications.