The use of cyanobacteria in biological wastewater treatment technologies can greatly reduce operation costs by combining wastewater bioremediation and production of lipid suitable as biodiesel feedstock. In this work, an attached growth system was employed to achieve the above-mentioned dual objective using a mixed microbial culture dominated by Leptolyngbya and Limnothrix species in diverse heterotrophic consortia. Kinetic experiments on different initial pollutant concentrations were carried out to determine the ability of the established culture to remove organic load (expressed by d-COD, dissolved-Chemical Oxygen Demand), N and P from agroindustrial wastewaters (dairy, winery and raisin). Biomass and oil productivity were determined. It was found that significant removal rates of nutrients were achieved in all the wastewaters examined, especially in that originated from winery in which the highest d-COD removal rate (up to 97.4%) was observed. The attached microbial biomass produced in winery wastewater contained 23.2% lipid/biomass, wt/wt, which was satisfying. The growth in the dairy wastewater yielded the highest attached biomass productivity (5.03 g m−2 day−1) followed by the mixed effluent of winery-raisin (4.12 g m−2 day−1) and the winery wastewater (3.08 g m−2 day−1). The produced microbial lipids contained high percentages of saturated and mono-unsaturated fatty acids (over 89% in total lipids) in all substrates examined. We conclude that the proposed attached growth photobioreactor system can be considered an effective wastewater treatment system that simultaneously produces microbial lipids suitable as biodiesel feedstock.