Microalgae has been shown to be promising for both wastewater treatment and the production of valuable biomass, which can be converted to sustainable biofuels, animal feeds, nutraceuticals, and food supplements. Previous research has demonstrated that a greater diversity of species can improve overall biomass productivity. Furthermore, biomass productivity and lipid composition is sensitive to cultivation conditions. In this study, we investigated the total lipid content and fatty acid composition of both assembled and naturally occurring algal communities that were cultivated in dairy wastewater. We extracted algal biomass using a chloroform:methanol (2:1) solution and total lipids were determined gravimetrically. We also examined two different extraction and derivatization methods that would be suitable for determining fatty acid profiles by gas chromatography-mass spectrometry. Fatty acid composition of algal biomass has important implications for biofuels.