Chlorococcum sp. RAP13—a fresh water microalga was evaluated for growth and lipid production in medium containing 50 % natural sea water under both phototrophic and heterotrophic cultivation modes. The algal cells adapted very well to the sea water and accumulated up to 38 % of their dry cell weight as lipids under heterotrophic cultivation. Biomass production and lipid accumulation were significantly higher than those in fresh water. Supplementation of biodiesel industry waste glycerol in sea water resulted in the highest yield of oil (330 mg L⁻¹), and the biomass yield was 0.85 g L⁻¹. The composition of oil produced under phototrophic and heterotrophic growth was significantly different, with the former enriched in polyunsaturated fatty acids while the latter contained more of medium chain saturated fatty acids and monounsaturated fatty acids suitable for biodiesel production. While the use of sea water reduces the requirement of mineral supplementation and saves fresh water, the ability to form oil from waste glycerol indicates the potential to recycle this waste. To the best of our knowledge, this is the first report on cultivation of the fresh water alga Chlorococcum sp. under heterotrophic mode in sea water.