The hydrodynamics of microbial aggregates, including settling velocity and permeability features, were investigated through detailed settling experiments. Microbial aggregates ranging from 1.0 to 2.5 mm were generated in a lab-scale sequencing batch reactor (SBR) and also collected from a full-scale activated sludge (AS) treatment process. An apparatus of vertically connected double settling columns, filled with solutions of different densities, was used to measure the settling velocities and thus to characterise the internal permeation of individual microbial aggregates. It was demonstrated that the microbial aggregates were highly porous and fractal. However, their settling velocities observed in deionised water, EDTA and NaCl solutions were only slightly faster than predicted by Stokes' law for identical but impermeable particles. The fluid collection efficiencies calculated from measured settling velocities were less than 0.10 for most microbial aggregates, which was much lower than those previously determined for non-biological aggregates of latex microspheres. It is suggested that microbial aggregates could have a largely reduced permeability, as the pores between the microorganisms in the aggregates may be clogged by the cell's exopolymeric material with the water retained.