The significantly increasing levels of Rare Earth Elements (REEs) in seawater are largely due to multiple anthropogenic activities. Their effects on marine primary producers such as Phaeodactylum tricornutum have not been fully assessed. This study focused on examining the long-term impacts of these two commonly occurring REEs, cerium (Ce) and gadolinium (Gd), on marine diatoms by 28 d of exposure. The 72 h effective concentrations that inhibited the growth of 20% (EC20) and 50% (EC50) of the exposed population were used for long-term exposures. The growth, oxidative stress level, photosynthetic pigments, and chlorophyll fluorescence were assessed in the diatoms, after 7, 14, 21, and 28 d of REEs exposure. Results display a difference in the toxicity induced by the two elements. Exposure to 2.39 mg/L (EC20) and 3.13 mg/L (EC50) of Ce, and to 4.52 mg/L (EC20) and 6.02 mg/L (EC50) of Gd displayed a lower effect on the growth of algae cells, as the response remained below 20% for inhibition or stimulation. Except for GD, the ROS and the activities of SOD, and LPO showed, during the exposure, comparable levels respect to control cells. A change in chlorophyll levels was also observed especially under Ce exposure. Both elements showed changes in photosynthetic performance. This study provides new insights into the different effects of Ce and Gd on P. tricornutum, demonstrating their diverse modes of action on this important primary producer. The findings provide further evidence of the adverse effects of anthropogenic REEs pollution on marine ecosystems.