Radial microscale distributions of oxygen and pH were studied in ca 1.5 mm large laboratory-made aggregates composed of phytoplankton detritus and fecal pellets. Microsensor measurements were done at spatial increments down to 0.05 mm in a vertical flow system in which the individual aggregates stabilized their position in the water phase according to the upward flow velocity. The aggregates were surrounded by a diffusive boundary layer with steep gradients of oxygen and pH. They were highly heterotrophic communities both under natural light conditions and in darkness. pH was lowered from 8.2 in the surrounding water to 7.4 in the center of an anoxic aggregate. Sulfide was not detectable by use of sulfide microelectrodes in anoxic aggregates, and methanogenic bacteria could not be detected after PCR (polymerase chain reaction) amplification using archaebacterial-specific primers. The oxygen respiration rate decreased exponentially over time with a T_1/2 of 2.3 d. Theoretical calculations of the volumetric oxygen respiration rate needed to deplete oxygen inside aggregates was compared to the density of organic matter in natural marine aggregates. These calculations showed that carbon limitation of heterotrophic processes would limit anoxic conditions to occurring only over a few hours, depending on the size of the aggregates. Therefore slow-growing obligate anaerobic microorganisms such as sulfate reducing bacteria and methanogenic bacteria may be limited by the relatively short persistence of anoxia in marine aggregates.