Coal excavation is associated with discharge of an enormous amount of mine water rich in salt and trace metal ions, which require efficient treatment before use. Considering the potentiality of microalgae for high salt tolerance, salt removal and metallic pollutant removal from aqueous system, present study focuses semi-continuous cultivation of candidate microalgae Chlorella pyrenoidosa (NCIM 2738) in bubble column reactor (BCR) and open raceway pond (ORP) for nutrient supplemented coal mine effluent (NSCME) treatment. In between different hydraulic retention times (HRTs), HRT 6 d provide maximum average biomass productivity of 950 mg L−1 d−1 in BCR and 728.4 mg L−1 d−1 in ORP. HRT 9 d facilitates a maximum lipid content of 1.8 g L ̶ 1 in BCR and 1.4 g L ̶ 1 in ORP. Further, HRT 9 d had the maximum COD removal efficiency (96.5 % in BCR and 94.2 % in ORP) and maximum salinity removal efficiency (93 % in BCR and 92 % in ORP). Fatty acid methyl esters (FAME) characterization highlighted potential biodiesel applicability with cetane number (CN) of 53.94. Energy dispersive X-ray spectroscopy (EDS) revealed an excess amount of salt and metal ions deposition on the surface of harvested microalgae samples. Outdoor large-scale C. pyrenoidosa cultivation can be integrated with coal mine closure plans to meet sustainable development goals (SDGs) 6, 7 and 13.