In this study, we set out to understand environmental effects on basic cell physiology as well as on the relationship between fatty acid and pigment constituents. Closed culturing environments were applied to grow Thalassiosira pseudonana under a temperature and irradiance matrix. It was demonstrated that the experimental parameters had a profound effect on cell physiology as well as cell biochemistry. We detected an inverse relationship between the expression of fatty acids and pigments from exponential to stationary phase growth; pigments were expressed at the highest concentrations during exponential growth and with the onset of stationary phase growth, there was a significant decrease in pigment concentrations that were mainly attributed to a sharp decline in chlorophyll-a. During stationary phase, changes in irradiance had the most dramatic effect at 18.0°C with 55% increase in lipid concentration from low to high irradiance. This increase in lipids was also reflected in a 20% increase in the average cell sizes from 4.8[mu]m to 5.4[mu]m and a 50% decrease in chlorophyll-a concentrations. Temperature and irradiance also had a significant effect on both fatty acid and pigment moieties. During stationary phase, the ratio of palmitic and palmitoleic acid (C16/C16:1) was closely regulated by both temperature and irradiance. A synergistic relationship was observed for temperature and saturated fatty acids and the inverse was detected for polyunsaturated fats. The ratio of photoprotective pigments to photosynthetic pigments (PP/PS) increased as a function of both temperature and irradiance during stationary phase, increasing most dramatically at higher temperatures and irradiances. These findings were able to give some insight in cellular lipid biochemistry in response to fluctuations in temperature and irradiance