Accumulated doses of natural ionizing radiation can be substantial over geological time scales. Based on the natural abundance of radionuclides, we calculated a typical dose rate of 0.04 Gy/ky in sea water, and 3.2-9.3 Gy/ky in marine sediments. We conducted a series of irradiation experiments using peat pore water and marine water and sediment samples. Fourier-Transform Ion Cyclotron mass spectrometry and lipid analysis was applied to elucidate changes in the molecular composition of organic matter by radiation, in dependence of dose and irradiation environment. While we find that the direct effect of radiation in the deep-sea is negligible even over the 5,000 years typical water residence time of organic matter, we see significant chemical changes, such as an increase of the average molecular oxygen content, after radiation doses that correspond to only several 10,000 years in marine sediments. We conclude that modification of organic matter by natural radioactivity is an important process over geological time scales, which affects the structure of any fossil organic matter older than several 10,000 years in a systematic way.