The aim of this dissertation is to examine how changes in the environment affect phytoplankton in terms of the quality and quantity of produced organic matter. For the first time, lipid classes were systematically examined as stress markers in cultures of diatoms Chaetoceros pseudocurvisetus and environmental water samples of different trophic statuses, the Adriatic Sea, the Wengchang River, China, and the Krka River, Croatia, estuaries. Among the environmental stress parameters, the effects of temperature and salinity changes and lack of nutrients were investigated. Thin layer chromatography and mass spectrometry methods were used for lipid analysis. The results obtained from cultivation experiments and field samples were compared and showed that under stressful conditions there is reduced phytoplankton growth, phytoplankton accumulate more lipids and excrete more dissolved organic matter including lipids. Remodeling of lipids occurs as a change in the ratio of phospholipids and glycolipids as a response to phosphate deficiency and the accumulation of triglycerides in the absence of nitrates in the growth medium. The change in salinity leads to changes in the fatty acid composition of phospholipids. The diatoms genus Chaetoceros has proven to be a good model organism for understanding the adaptation of phytoplankton to global changes.