Flexible responses of lipid metabolism to changes in cultivation conditions characteristic of oleaginous microalgae of the genus Nannochloropsis render them a promising source of triacylglycerols for biodiesel (under nutrient-deprivation and high-light stress) and eicosapentaenoic acid (EPA; C20:5, n-3) (under nutrient sufficient conditions). We investigated the responses of fatty acid and pigment profile in the euryhaline Nannochloropsis oceanica CCALA 804 to the combined stresses of high light (HL), salinity (0, 27, and 40 g/L NaCl) and nitrogen deprivation. The growth in nitrogen-replete medium under HL triggered a rapid acclimation of the microalgae to the HL stress in a salinity-dependent manner associated with a moderate decrease of EPA proportion of total FA. Nitrogen starvation (i) slowed the biomass accumulation, (ii) enhanced the production of reserve lipids at the expense of chloroplast lipids, and (iii) triggered photoprotective responses of pigment apparatus in N. oceanica. Regardless of cultivation conditions, the stress-induced changes in pigments and fatty acid profile were highly coordinated. Nitrogen-starvation promoted total FA accumulation on the background of a marked decline in EPA and light-harvesting Car as well as up-regulation of violaxanthin cycle with concomitant rise in non-photochemical quenching. Zero-NaCl conditions appeared to be beneficial for biomass and EPA accumulation and alleviated, especially under nitrogen starvation, the effects of salinity stresses (the decline in biomass accumulation rate, content of light-harvesting carotenoids and EPA, and photosynthetic efficiency). Strategies of N. oceanica acclimation to stresses of different nature and their possible implications for the biotechnology of this species are discussed.