Thalassiosira hyalina and Nitzschia frigida are important members of Arctic pelagic and sympagic (sea‐ice‐associated) diatom communities. We investigated the effects of light stress (shift from 20 to 380 µmol photons m−2 s−1, resembling upwelling or ice break‐up) under contemporary and future pCO2 (400 vs 1000 µatm). The responses in growth, elemental composition, pigmentation and photophysiology were followed over 120 h and are discussed together with underlying gene expression patterns. Stress response and subsequent re-acclimation were efficiently facilitated by T. hyalina, which showed only moderate changes in photophysiology and elemental composition, and thrived under high light after 120 h. In N. frigida, photochemical damage and oxidative stress appeared to outweigh cellular defenses, causing dysfunctional photophysiology and reduced growth. pCO2 alone did not specifically influence gene expression, but amplified the transcriptomic reactions to light stress, indicating that pCO2 affects metabolic equilibria rather than sensitive genes. Large differences in acclimation capacities towards high light and high pCO2 between T. hyalina and N. frigida indicate species‐specific mechanisms in coping with the two stressors, which may reflect their respective ecological niches. This could potentially alter the balance between sympagic and pelagic primary production in a future Arctic.