In the frame of studies on the safe disposal of nuclear waste, there is a great interest for understanding the migration behavior of 99Tc. 99Tc originating from nuclear energy production and global fallout shows environmental levels down to 107 atoms/g of soil (∼2 fg/g). Extremely low concentrations are also expected in groundwater after diffusion of 99Tc through the bentonite constituting the technical barrier for nuclear waste disposal. The main limitation to the sensitivity of the mass spectrometric analysis of 99Tc is the background of its stable isobar 99Ru. For ultratrace analysis, the Accelerator Mass Spectrometry (AMS) setup of the Technical University of Munich using a Gas-Filled Analyzing Magnet System (GAMS) and a 14 MV Tandem accelerator is greatly effective in suppressing this interference. In the present study, the GAMS setup is used for the analysis of 99Tc in samples of the seawater reference material IAEA-443, a peat bog lake, and groundwater from an experiment of in situ diffusion through bentonite in the controlled zone of the Grimsel Test Site (GTS) within the Colloid Formation and Migration (CFM) project. With an adapted chemical preparation procedure, measurements of 99Tc concentrations at the fg/g levels with a sensitivity down to 0.5 fg are accomplished in notably small natural water samples. The access to these low concentration levels allows for the long-term monitoring of in situ tracer tests over several years and for the determination of environmental levels of 99Tc in small samples.