Since land-based biofuel production competes with conventional food production, a water-based biomass and biofuel production from cyanobacteria offers large potential. This study investigates the application potential of cyanobacteria for fuel production and by-products by mimicking nutrient depleted environmental conditions. Three Baltic cyanobacteria strains (Aphanizomenon flos-aquae, Dolichospermum lemmermannii and Nodularia spumigena) were inoculated in full nutrient levels, as well as phosphorus and nitrogen depleted medium, before being monitored for 14 days. For screening reasons, multiple parameters such as fatty acids, photosynthetic pigments including phycobilins, biovolume, photosynthetic activity, inorganic nutrients, particulate organic carbon, nitrogen and phosphorous were investigated every seven days. We observed a strong negative relationship between lipid content, growth and nutrient availability, resulting in high lipid and pigment production in combination with a limited growth rate in nutrient depleted treatments. Our results suggest that cultivation and harvest of bloom-forming cyanobacteria for fuel and by-product production are feasible in Scandinavia, but strongly depends on the desired compounds and biomass. Each cyanobacteria species originally has a species-specific chemical fingerprint that may be modified by rearing conditions and harvesting period to meet the needs of the consumer. This leads to important conclusions regarding future culturing conditions and biomass production of the desired compounds.