Second cheese whey (SCW), a by-product generated after the production of cottage cheese, remains a highly polluted effluent due to its high organic and nutrient load. Despite its environmental impact, the biotreatment of SCW using microalgae/cyanobacteria has been limited, with even fewer studies involving pilot-scale photobioreactors. In this study, unsterilized SCW was treated employing a Leptolyngbya-based culture in two pilot-scale systems: a suspended growth system (SCW-S) and an attached growth system (SCW-A), both operated in 9 L tubular photobioreactors. For the attached system, fishing lines equipped with plastic biofilm carriers served as support material for microbial attachment. Leptolyngbya sp. is known to increase lipid content at C:N ratios of ≈ 45; thus, SCW was studied under these conditions, with an initial d-COD of about 2000 mg L⁻¹. The highest total biomass productivity was observed in SCW-A system, reaching 346.7 mg L⁻¹d⁻¹. Both systems achieved high effectiveness in pollutant removal (d-COD: 94.5-99.9%, TN: 89.0-96.5%, ΝΟ₃⁻-Ν: 87.0-93.3%, PO₄³⁻: 98.8-93.4%), while lipid contents were 16.1 and 15.1% d.w. for SCW-S and SCW-A, respectively. SCW-A proved highly effective, achieving almost complete d-COD (99.9%) and TN (96.5%) removal. Lipid analysis revealed increased saturation of fatty acids in the SCW-A, representing 74.6% of total fatty acids. The attached system was also applied to synthetic chemical medium (CM-A) to evaluate lipid production potential. The CM-A recorded lower biomass productivity (142.8 mg L⁻¹d⁻¹) and lipid content (12.0 % d.w.), suggesting SCW’s indigenous microbiota enhanced growth and lipid production. In conclusion, SCW is an effective feedstock for lipid-rich biomass production with Leptolyngbya, yielding saturated lipids suitable for biofuels.